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As of 22-May-2019 number of released structures: 10174
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 5006  Download results as an excel file       Gallery view

NDB ID:

6R9J

PDB ID:

6R9J 

Release:

2019-05-22

Title:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with A7 RNA

Classification:

HYDROLASE

Authors:

Tang, T.T.L., Stowell, J.A.W., Hill, C.H., Passmore, L.A.

Citation:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
Nat.Struct.Mol.Biol. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.326Å R work:0.247R free:0.298

NDB ID:

6R9M

PDB ID:

6R9M 

Release:

2019-05-22

Title:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGAA RNA

Classification:

HYDROLASE

Authors:

Tang, T.T.L., Stowell, J.A.W., Hill, C.H., Passmore, L.A.

Citation:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
Nat.Struct.Mol.Biol. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.329Å R work:0.236R free:0.295

NDB ID:

6R9O

PDB ID:

6R9O 

Release:

2019-05-22

Title:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA

Classification:

HYDROLASE

Authors:

Tang, T.T.L., Stowell, J.A.W., Hill, C.H., Passmore, L.A.

Citation:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
Nat.Struct.Mol.Biol. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.319Å R work:0.254R free:0.309

NDB ID:

6R9P

PDB ID:

6R9P 

Release:

2019-05-22

Title:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAUUAA RNA

Classification:

HYDROLASE

Authors:

Tang, T.T.L., Stowell, J.A.W., Hill, C.H., Passmore, L.A.

Citation:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
Nat.Struct.Mol.Biol. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.98Å R work:0.261R free:0.308

NDB ID:

6R9Q

PDB ID:

6R9Q 

Release:

2019-05-22

Title:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AACCAA RNA

Classification:

HYDROLASE

Authors:

Tang, T.T.L., Stowell, J.A.W., Hill, C.H., Passmore, L.A.

Citation:

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module
Nat.Struct.Mol.Biol. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.079Å R work:0.26R free:0.296

NDB ID:

5ZUU

PDB ID:

5ZUU 

Release:

2019-05-15

Title:

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Wu, B.X., Nie, H.B., Li, S.S., Patel, D.J.

Citation:

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.95Å R work:0.199R free:0.255

NDB ID:

6N4O

PDB ID:

6N4O 

Release:

2019-05-08

Title:

Human Argonaute2-miR-122 bound to a seed and supplementary paired target

Classification:

RNA binding protein/rna

Authors:

Sheu-Gruttadauria, J., Xiao, Y., Gebert, L.F., MacRae, I.J.

Citation:

Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2.
Embo J. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.899Å R work:0.207R free:0.257

NDB ID:

6RA4

PDB ID:

6RA4 

Release:

2019-05-08

Title:

Human ARGONAUTE-2 PAZ DOMAIN (214-347) IN COMPLEX WITH CGUGACUCU

Classification:

RNA BINDING PROTEIN

Authors:

Greenidge, P., Blommers, M.J.J., Priestle, J.P., Hunziker, J.

Citation:

How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for De Novo siRNA Guide Strand Surrogate Selection.
J.Chem.Inf.Model. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.238R free:0.268

NDB ID:

6IBQ

PDB ID:

6IBQ 

Release:

2019-05-01

Title:

Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device

Classification:

RNA

Authors:

De Wijn, R., Henning, O., Roche, J., Engilberge, S., Betat, H., Morl, M., Roussel, A., Girard, E., Olieric, V., Fox, G.C., Brillet, K., Lorber, B., Sauter, C.

Citation:

New microfluidic design for crystallization of biomolecules and their in situ analysis by serial crystallography
Iucrj pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.55Å R work:0.192R free:0.222

NDB ID:

6DTI

PDB ID:

6DTI 

Release:

2019-04-24

Title:

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an unmodifed anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin

Classification:

RIBOSOME

Authors:

Cantara, W.A., Vangaveti, S., Sarachan, K.L., Spears, J.L., DeMirci, H., Murphy IV, F.V., Ranganathan, S.V., Agris, P.F.

Citation:

A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.54Å R work:0.196R free:0.235

NDB ID:

6HYK

PDB ID:

6HYK 

Release:

2019-04-24

Title:

NMR solution structure of the C/D box snoRNA U14

Classification:

RNA

Authors:

Chagot, M.E., Quinternet, M., Rothe, B., Charpentier, B., Coutant, J., Manival, X., Lebars, I.

Citation:

The yeast C/D box snoRNA U14 adopts a ""weak"" K-turn like conformation recognized by the Snu13 core protein in solution.
Biochimie pp. - 2019

Experiment:

SOLUTION NMR

NDB ID:

6MKN

PDB ID:

6MKN 

Release:

2019-04-24

Title:

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin

Classification:

RIBOSOME

Authors:

Cantara, W.A., Vangaveti, S., Sarachan, K.L., Spears, J.L., DeMirci, H., Murphy IV, F.V., Ranganathan, S.V., Agris, P.F.

Citation:

A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.46Å R work:0.202R free:0.233

NDB ID:

6MPF

PDB ID:

6MPF 

Release:

2019-04-24

Title:

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin

Classification:

RIBOSOME

Authors:

Cantara, W.A., Vangaveti, S., Sarachan, K.L., Spears, J.L., DeMirci, H., Murphy IV, F.V., Ranganathan, S.V., Agris, P.F.

Citation:

A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.33Å R work:0.177R free:0.218

NDB ID:

6MPI

PDB ID:

6MPI 

Release:

2019-04-24

Title:

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGU-codon in the A-site and paromomycin

Classification:

RIBOSOME

Authors:

Cantara, W.A., Vangaveti, S., Sarachan, K.L., Spears, J.L., DeMirci, H., Murphy IV, F.V., Ranganathan, S.V., Agris, P.F.

Citation:

A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.33Å R work:0.19R free:0.216

NDB ID:

6E8S

PDB ID:

6E8S 

Release:

2019-04-17

Title:

Structure of the iMango-III aptamer bound to TO1-Biotin

Classification:

RNA

Authors:

Trachman 3rd., R.J., Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.

Citation:

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat. Chem. Biol. 15 pp.472 - 479 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.35Å R work:0.182R free:0.207

Equivalence Class: 

NR_all_98433.1 

Eq. Class Rep:

6E8S

NDB ID:

6E8T

PDB ID:

6E8T 

Release:

2019-04-17

Title:

Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

Classification:

RNA

Authors:

Trachman 3rd., R.J., Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.

Citation:

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat. Chem. Biol. 15 pp.472 - 479 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.194R free:0.236

Equivalence Class: 

NR_all_14315.1 

Eq. Class Rep:

6E8T

NDB ID:

6E8T

PDB ID:

6E8T 

Release:

2019-04-17

Title:

Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

Classification:

RNA

Authors:

Trachman 3rd., R.J., Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.

Citation:

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat. Chem. Biol. 15 pp.472 - 479 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.194R free:0.236

Equivalence Class: 

NR_all_39458.1 

Eq. Class Rep:

6E8T

NDB ID:

6E8U

PDB ID:

6E8U 

Release:

2019-04-17

Title:

Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

Classification:

RNA

Authors:

Trachman 3rd., R.J., Autour, A., Jeng, S.C.Y., Abdolahzadeh, A., Andreoni, A., Cojocaru, R., Garipov, R., Dolgosheina, E.V., Knutson, J.R., Ryckelynck, M., Unrau, P.J., Ferre-D'Amare, A.R.

Citation:

Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat. Chem. Biol. 15 pp.472 - 479 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.55Å R work:0.176R free:0.206

Equivalence Class: 

NR_all_70791.1 

Eq. Class Rep:

6E8U

NDB ID:

6H0R

PDB ID:

6H0R 

Release:

2019-04-17

Title:

X-ray structure of SRS2 fragment of Rgs4 3' UTR

Classification:

RNA

Authors:

Heber, S., Gaspar, I., Tants, J.N., Gunther, J., Moya, S.M.F., Janowski, R., Ephrussi, A., Sattler, M., Niessing, D.

Citation:

Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains.
Nat Commun 10 pp.1659 - 1659 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.73Å R work:0.184R free:0.237

Equivalence Class: 

NR_all_13447.1 

Eq. Class Rep:

6H0R

NDB ID:

6JOO

PDB ID:

6JOO 

Release:

2019-04-17

Title:

Crystal structure of Corynebacterium diphtheriae Cas9 in complex with sgRNA and target DNA

Classification:

HYDROLASE/DNA/RNA

Authors:

Hirano, S., Abudayyeh, O.O., Gootenberg, J.S., Horii, T., Ishitani, R., Hatada, I., Zhang, F., Nishimasu, H., Nureki, O.

Citation:

Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9.
Nat Commun 10 pp.1968 - 1968 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.22R free:0.253

Equivalence Class: 

NR_all_62361.1 

Eq. Class Rep:

6JOO

NDB ID:

6O16

PDB ID:

6O16 

Release:

2019-04-17

Title:

Crystal structure of murine DHX37 in complex with RNA

Classification:

HYDROLASE/RNA

Authors:

Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U., Jinek, M.

Citation:

Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14 in ribosome biogenesis.
RNA pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.875Å R work:0.27R free:0.294

Equivalence Class: 

NR_all_58704.1 

Eq. Class Rep:

6O16

NDB ID:

6O97

PDB ID:

6O97 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Matsushita, T., Sati, G.C., Kondasinghe, N., Pirrone, M.G., Kato, T., Waduge, P., Kumar, H.S., Sanchon, A.C., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S.N., Schrepfer, T., Chow, C.S., Polikanov, Y.S., Schacht, J., Vasella, A., Bottger, E.C., Crich, D.

Citation:

Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc. 141 pp.5051 - 5061 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_65795.47 

Eq. Class Rep:

4LFB

NDB ID:

6O97

PDB ID:

6O97 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Matsushita, T., Sati, G.C., Kondasinghe, N., Pirrone, M.G., Kato, T., Waduge, P., Kumar, H.S., Sanchon, A.C., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S.N., Schrepfer, T., Chow, C.S., Polikanov, Y.S., Schacht, J., Vasella, A., Bottger, E.C., Crich, D.

Citation:

Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc. 141 pp.5051 - 5061 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_97519.43 

Eq. Class Rep:

4Y4O

NDB ID:

6O97

PDB ID:

6O97 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Matsushita, T., Sati, G.C., Kondasinghe, N., Pirrone, M.G., Kato, T., Waduge, P., Kumar, H.S., Sanchon, A.C., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S.N., Schrepfer, T., Chow, C.S., Polikanov, Y.S., Schacht, J., Vasella, A., Bottger, E.C., Crich, D.

Citation:

Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc. 141 pp.5051 - 5061 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_42622.43 

Eq. Class Rep:

5FDV

NDB ID:

6O97

PDB ID:

6O97 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Matsushita, T., Sati, G.C., Kondasinghe, N., Pirrone, M.G., Kato, T., Waduge, P., Kumar, H.S., Sanchon, A.C., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S.N., Schrepfer, T., Chow, C.S., Polikanov, Y.S., Schacht, J., Vasella, A., Bottger, E.C., Crich, D.

Citation:

Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc. 141 pp.5051 - 5061 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_35542.59 

Eq. Class Rep:

5L4O

NDB ID:

6O97

PDB ID:

6O97 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolution

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Matsushita, T., Sati, G.C., Kondasinghe, N., Pirrone, M.G., Kato, T., Waduge, P., Kumar, H.S., Sanchon, A.C., Dobosz-Bartoszek, M., Shcherbakov, D., Juhas, M., Hobbie, S.N., Schrepfer, T., Chow, C.S., Polikanov, Y.S., Schacht, J., Vasella, A., Bottger, E.C., Crich, D.

Citation:

Design, Multigram Synthesis, and in Vitro and in Vivo Evaluation of Propylamycin: A Semisynthetic 4,5-Deoxystreptamine Class Aminoglycoside for the Treatment of Drug-Resistant Enterobacteriaceae and Other Gram-Negative Pathogens.
J. Am. Chem. Soc. 141 pp.5051 - 5061 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.75Å R work:0.235R free:0.284

Equivalence Class: 

NR_all_69813.7 

Eq. Class Rep:

6OF1

NDB ID:

6OF1

PDB ID:

6OF1 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

Classification:

RIBOSOME

Authors:

Khabibullina, N.F., Tereshchenkov, A.G., Komarova, E.S., Syroegin, E.A., Shiriaev, D.I., Paleskava, A., Kartsev, V.G., Bogdanov, A.A., Konevega, A.L., Dontsova, O.A., Sergiev, P.V., Osterman, I.A., Polikanov, Y.S.

Citation:

Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.
Antimicrob. Agents Chemother. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.262

Equivalence Class: 

NR_all_65795.47 

Eq. Class Rep:

4LFB

NDB ID:

6OF1

PDB ID:

6OF1 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

Classification:

RIBOSOME

Authors:

Khabibullina, N.F., Tereshchenkov, A.G., Komarova, E.S., Syroegin, E.A., Shiriaev, D.I., Paleskava, A., Kartsev, V.G., Bogdanov, A.A., Konevega, A.L., Dontsova, O.A., Sergiev, P.V., Osterman, I.A., Polikanov, Y.S.

Citation:

Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.
Antimicrob. Agents Chemother. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.262

Equivalence Class: 

NR_all_97519.43 

Eq. Class Rep:

4Y4O

NDB ID:

6OF1

PDB ID:

6OF1 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

Classification:

RIBOSOME

Authors:

Khabibullina, N.F., Tereshchenkov, A.G., Komarova, E.S., Syroegin, E.A., Shiriaev, D.I., Paleskava, A., Kartsev, V.G., Bogdanov, A.A., Konevega, A.L., Dontsova, O.A., Sergiev, P.V., Osterman, I.A., Polikanov, Y.S.

Citation:

Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.
Antimicrob. Agents Chemother. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.262

Equivalence Class: 

NR_all_42622.43 

Eq. Class Rep:

5FDV

NDB ID:

6OF1

PDB ID:

6OF1 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

Classification:

RIBOSOME

Authors:

Khabibullina, N.F., Tereshchenkov, A.G., Komarova, E.S., Syroegin, E.A., Shiriaev, D.I., Paleskava, A., Kartsev, V.G., Bogdanov, A.A., Konevega, A.L., Dontsova, O.A., Sergiev, P.V., Osterman, I.A., Polikanov, Y.S.

Citation:

Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.
Antimicrob. Agents Chemother. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.262

Equivalence Class: 

NR_all_35542.59 

Eq. Class Rep:

5L4O

NDB ID:

6OF1

PDB ID:

6OF1 

Release:

2019-04-17

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolution

Classification:

RIBOSOME

Authors:

Khabibullina, N.F., Tereshchenkov, A.G., Komarova, E.S., Syroegin, E.A., Shiriaev, D.I., Paleskava, A., Kartsev, V.G., Bogdanov, A.A., Konevega, A.L., Dontsova, O.A., Sergiev, P.V., Osterman, I.A., Polikanov, Y.S.

Citation:

Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.
Antimicrob. Agents Chemother. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.262

Equivalence Class: 

NR_all_69813.7 

Eq. Class Rep:

6OF1

NDB ID:

6CZR

PDB ID:

6CZR 

Release:

2019-04-10

Title:

The structure of amicetin bound to the 70S ribosome

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Serrano, C.M., Kannareddy, H.R., Eiler, D.R., Koch, M.R., Barrows, L.R., Testa, C.A., Sebahar, P.R., Looper, R.E.

Citation:

Unifying aminohexopyranose nucleoside antibiotics: implications for antibiotic design
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.14Å R work:0.238R free:0.291

Equivalence Class: 

NR_all_97519.43 

Eq. Class Rep:

4Y4O

NDB ID:

6CZR

PDB ID:

6CZR 

Release:

2019-04-10

Title:

The structure of amicetin bound to the 70S ribosome

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Serrano, C.M., Kannareddy, H.R., Eiler, D.R., Koch, M.R., Barrows, L.R., Testa, C.A., Sebahar, P.R., Looper, R.E.

Citation:

Unifying aminohexopyranose nucleoside antibiotics: implications for antibiotic design
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.14Å R work:0.238R free:0.291

Equivalence Class: 

NR_all_42622.43 

Eq. Class Rep:

5FDV

NDB ID:

6CZR

PDB ID:

6CZR 

Release:

2019-04-10

Title:

The structure of amicetin bound to the 70S ribosome

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Serrano, C.M., Kannareddy, H.R., Eiler, D.R., Koch, M.R., Barrows, L.R., Testa, C.A., Sebahar, P.R., Looper, R.E.

Citation:

Unifying aminohexopyranose nucleoside antibiotics: implications for antibiotic design
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.14Å R work:0.238R free:0.291

Equivalence Class: 

NR_all_98268.1 

Eq. Class Rep:

6CZR

NDB ID:

6E1S

PDB ID:

6E1S 

Release:

2019-04-10

Title:

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine

Classification:

RNA

Authors:

Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferre-D'Amare, A.R., Schneekloth Jr., J.S.

Citation:

Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 pp.1501 - 1501 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.196R free:0.204

Equivalence Class: 

NR_all_80276.1 

Eq. Class Rep:

6E1S

NDB ID:

6E1T

PDB ID:

6E1T 

Release:

2019-04-10

Title:

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 1: 2-[(dibenzo[b,d]furan-2-yl)oxy]ethan-1-amine

Classification:

RNA

Authors:

Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferre-D'Amare, A.R., Schneekloth Jr., J.S.

Citation:

Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 pp.1501 - 1501 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.195R free:0.204

Equivalence Class: 

NR_all_80276.1 

Eq. Class Rep:

6E1S

NDB ID:

6E1U

PDB ID:

6E1U 

Release:

2019-04-10

Title:

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 2: 2-[(dibenzo[b,d]furan-2-yl)oxy]-N,N-dimethylethan-1-amine

Classification:

RNA

Authors:

Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferre-D'Amare, A.R., Schneekloth Jr., J.S.

Citation:

Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 pp.1501 - 1501 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.94Å R work:0.189R free:0.202

Equivalence Class: 

NR_all_80276.1 

Eq. Class Rep:

6E1S

NDB ID:

6E1V

PDB ID:

6E1V 

Release:

2019-04-10

Title:

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine

Classification:

RNA

Authors:

Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferre-D'Amare, A.R., Schneekloth Jr., J.S.

Citation:

Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 pp.1501 - 1501 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.56Å R work:0.239R free:0.247

Equivalence Class: 

NR_all_80276.1 

Eq. Class Rep:

6E1S

NDB ID:

6E1W

PDB ID:

6E1W 

Release:

2019-04-10

Title:

Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1

Classification:

RNA

Authors:

Connelly, C.M., Numata, T., Boer, R.E., Moon, M.H., Sinniah, R.S., Barchi, J.J., Ferre-D'Amare, A.R., Schneekloth Jr., J.S.

Citation:

Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun 10 pp.1501 - 1501 2019

Experiment:

X-RAY DIFFRACTION Resolution:1.69Å R work:0.18R free:0.21

Equivalence Class: 

NR_all_80276.1 

Eq. Class Rep:

6E1S

NDB ID:

6G3B

PDB ID:

6G3B 

Release:

2019-04-10

Title:

AvaII restriction endonuclease in complex with an RNA/DNA hybrid

Classification:

HYDROLASE

Authors:

Kisiala, M., Kowalska, M., Czapinska, H., Bochtler, M.

Citation:

Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.167R free:0.202

Equivalence Class: 

NR_all_86801.1 

Eq. Class Rep:

6G3B

NDB ID:

6JIM

PDB ID:

6JIM 

Release:

2019-04-10

Title:

Viral helicase protein

Classification:

VIRAL PROTEIN/RNA

Authors:

Law, Y.S., Utt, A., Tan, Y.B., Zheng, J., Wang, S., Chen, M.W., Griffin, P.R., Merits, A., Luo, D.

Citation:

Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase.
Proc.Natl.Acad.Sci.USA 116 pp.9558 - 9567 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.177R free:0.215

Equivalence Class: 

NR_all_60948.1 

Eq. Class Rep:

6JIM

NDB ID:

5ZKJ

PDB ID:

5ZKJ 

Release:

2019-04-03

Title:

Human EXOG-H140A in complex with RNA/DNA hybrid duplex

Classification:

HYDROLASE/RNA/DNA

Authors:

Wu, C.C., Lin, J.L.J., Yang-Yen, H.F., Yuan, H.S.

Citation:

A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Nucleic Acids Res. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.798Å R work:0.18R free:0.226

Equivalence Class: 

NR_all_17854.1 

Eq. Class Rep:

5ZKJ

NDB ID:

6HAK

PDB ID:

6HAK 

Release:

2019-04-03

Title:

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with a double stranded RNA represents the RT transcription initiation complex prior to nucleotide incorporation

Classification:

TRANSCRIPTION

Authors:

Das, K., Martinez, S.E., DeStefano, J.J., Arnold, E.

Citation:

Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation.
Proc.Natl.Acad.Sci.USA 116 pp.7308 - 7313 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.95Å R work:0.293R free:0.328

Equivalence Class: 

NR_all_63549.1 

Eq. Class Rep:

6HAK

NDB ID:

6IID

PDB ID:

6IID 

Release:

2019-04-03

Title:

Human EXOG-H140A in complex with RNA-DNA chimeric duplex

Classification:

HYDROLASE/DNA

Authors:

Wu, C.C., Lin, J.L.J., Yang-Yen, H.F., Yuan, H.S.

Citation:

A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Nucleic Acids Res. pp. - 2019

Experiment:

X-RAY DIFFRACTION Resolution:2.986Å R work:0.199R free:0.252

NDB ID:

6N1D

PDB ID:

6N1D 

Release:

2019-04-03

Title:

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Classification:

RIBOSOME

Authors:

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Citation:

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 pp.7813 - 7818 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.268R free:0.321

Equivalence Class: 

NR_all_65795.47 

Eq. Class Rep:

4LFB

NDB ID:

6N1D

PDB ID:

6N1D 

Release:

2019-04-03

Title:

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Classification:

RIBOSOME

Authors:

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Citation:

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 pp.7813 - 7818 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.268R free:0.321

Equivalence Class: 

NR_all_89292.3 

Eq. Class Rep:

4WQ1

NDB ID:

6N1D

PDB ID:

6N1D 

Release:

2019-04-03

Title:

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Classification:

RIBOSOME

Authors:

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Citation:

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 pp.7813 - 7818 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.268R free:0.321

Equivalence Class: 

NR_all_97519.43 

Eq. Class Rep:

4Y4O

NDB ID:

6N1D

PDB ID:

6N1D 

Release:

2019-04-03

Title:

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Classification:

RIBOSOME

Authors:

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Citation:

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 pp.7813 - 7818 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.268R free:0.321

Equivalence Class: 

NR_all_42622.43 

Eq. Class Rep:

5FDV

NDB ID:

6N1D

PDB ID:

6N1D 

Release:

2019-04-03

Title:

X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid State

Classification:

RIBOSOME

Authors:

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Citation:

Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state.
Proc. Natl. Acad. Sci. U.S.A. 116 pp.7813 - 7818 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.268R free:0.321

Equivalence Class: 

NR_all_69813.7 

Eq. Class Rep:

6OF1

NDB ID:

6AEB

PDB ID:

6AEB 

Release:

2019-03-27

Title:

Crystal structure of xCas9 in complex with sgRNA and target DNA (AAG PAM)

Classification:

DNA BINDING PROTEIN/RNA

Authors:

Guo, M., Ren, K., Zhu, Y., Tang, Z., Wang, Y., Zhang, B., Huang, Z.

Citation:

Structural insights into a high fidelity variant of SpCas9.
Cell Res. 29 pp.183 - 192 2019

Experiment:

X-RAY DIFFRACTION Resolution:3.004Å R work:0.231R free:0.282

Equivalence Class: 

NR_all_92081.6 

Eq. Class Rep:

5FQ5