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As of 15-May-2018 number of released structures: 9482
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4530  Download results as an excel file       Gallery view

NDB ID:

5NPM

PDB ID:

5NPM 

Release:

2018-05-16

Title:

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

Classification:

RNA

Authors:

Gabdulkhakov, A.G., Tishchenko, T.V., Nevskaya, N.A., Nikonov, S.V., Garber, M.B.

Citation:

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.201R free:0.248

NDB ID:

5VSU

PDB ID:

5VSU 

Release:

2018-05-09

Title:

Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA

Classification:

SPLICING

Authors:

Montemayor, E.J., Didychuk, A.L., Yake, A.D., Sidhu, G.K., Brow, D.A., Butcher, S.E.

Citation:

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Nat Commun 9 pp.1749 - 1749 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.233R free:0.298

NDB ID:

6ASO

PDB ID:

6ASO 

Release:

2018-05-09

Title:

Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA

Classification:

SPLICING

Authors:

Montemayor, E.J., Didychuk, A.L., Yake, A.D., Sidhu, G.K., Brow, D.A., Butcher, S.E.

Citation:

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Nat Commun 9 pp.1749 - 1749 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.71Å R work:0.194R free:0.246

NDB ID:

6FPQ

PDB ID:

6FPQ 

Release:

2018-05-09

Title:

Structure of S. pombe Mmi1 in complex with 7-mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Stowell, J.A.W., Wagstaff, J.L., Hill, C.H., Yu, M., McLaughlin, S.H., Freund, S.M.V., Passmore, L.A.

Citation:

A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.
J. Biol. Chem. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.42Å R work:0.142R free:0.167

NDB ID:

6FPX

PDB ID:

6FPX 

Release:

2018-05-09

Title:

Structure of S. pombe Mmi1 in complex with 11-mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Stowell, J.A.W., Wagstaff, J.L., Hill, C.H., Yu, M., McLaughlin, S.H., Freund, S.M.V., Passmore, L.A.

Citation:

A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.
J. Biol. Chem. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.97Å R work:0.2R free:0.234

NDB ID:

6FQ3

PDB ID:

6FQ3 

Release:

2018-05-09

Title:

Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with lin-29A 5'UTR 13mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Kumari, P., Aeschimann, F., Gaidatzis, D., Keusch, J.J., Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H., Grosshans, H., Ciosk, R.

Citation:

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Nat Commun 9 pp.1549 - 1549 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.901Å R work:0.158R free:0.18

NDB ID:

6FQL

PDB ID:

6FQL 

Release:

2018-05-09

Title:

Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with mab-10 3'UTR 13mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Kumari, P., Aeschimann, F., Gaidatzis, D., Keusch, J.J., Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H., Grosshans, H., Ciosk, R.

Citation:

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Nat Commun 9 pp.1549 - 1549 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.349Å R work:0.171R free:0.21

NDB ID:

5NDJ

PDB ID:

5NDJ 

Release:

2018-05-02

Title:

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

Classification:

RIBOSOME

Authors:

Prokhorova, I., Altman, R.B., Djumagulov, M., Shrestha, J.P., Urzhumtsev, A., Ferguson, A., Chang, C.T., Yusupov, M., Blanchard, S.C., Yusupova, G.

Citation:

Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.E10899 - E10908 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.15Å R work:0.202R free:0.246

NDB ID:

5USB

PDB ID:

5USB 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (rGGTTACGGT)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.615Å R work:0.175R free:0.202

NDB ID:

5USN

PDB ID:

5USN 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (rGrGrUTACGGT)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.183R free:0.223

NDB ID:

5USO

PDB ID:

5USO 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (GGTTACrGrGrU)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.21R free:0.245

NDB ID:

5XPA

PDB ID:

5XPA 

Release:

2018-04-18

Title:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand

Classification:

DNA BINDING PROTEIN

Authors:

Sheng, G., Gogakos, T., Wang, J., Zhao, H., Serganov, A., Juranek, S., Tuschl, T., Patel, J.D., Wang, Y.

Citation:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.215R free:0.28

NDB ID:

5XPG

PDB ID:

5XPG 

Release:

2018-04-18

Title:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand

Classification:

DNA BINDING PROTEIN

Authors:

Sheng, G., Gogakos, T., Wang, J., Zhao, H., Serganov, A., Juranek, S., Tuschl, T., Patel, J.D., Wang, Y.

Citation:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.202R free:0.246

NDB ID:

6CAE

PDB ID:

6CAE 

Release:

2018-04-18

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution

Classification:

RIBOSOME/INHIBITOR

Authors:

Pantel, L., Florin, T., Dobosz-Bartoszek, M., Racine, E., Sarciaux, M., Serri, M., Houard, J., Campagne, J.M., de Figueiredo, R.M., Midrier, C., Gaudriault, S., Givaudan, A., Lanois, A., Forst, S., Aumelas, A., Cotteaux-Lautard, C., Bolla, J.M., Vingsbo Lundberg, C., Huseby, D.L., Hughes, D., Villain-Guillot, P., Mankin, A.S., Polikanov, Y.S., Gualtieri, M.

Citation:

Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site.
Mol. Cell 70 pp.83 - 94.e7 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.211R free:0.249

NDB ID:

6CBD

PDB ID:

6CBD 

Release:

2018-04-18

Title:

Crystal Structure of Human Argonaute2 Bound to Three Tryptophans

Classification:

RNA BINDING PROTEIN

Authors:

Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Phase Transitions in the Assembly and Function of Human miRISC.
Cell 173 pp.946 - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.203Å R work:0.175R free:0.215

NDB ID:

6C6K

PDB ID:

6C6K 

Release:

2018-04-04

Title:

Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Johnson, B., VanBlargan, L.A., Xu, W., White, J.P., Shan, C., Shi, P.Y., Zhang, R., Adhikari, J., Gross, M.L., Leung, D.W., Diamond, M.S., Amarasinghe, G.K.

Citation:

Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability.
Immunity 48 pp.487 - 499.e5 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.54Å R work:0.168R free:0.236

NDB ID:

5V8I

PDB ID:

5V8I 

Release:

2018-03-28

Title:

Thermus thermophilus 70S ribosome lacking ribosomal protein uS17

Classification:

RIBOSOME

Authors:

Murphy, E., Connetti, J.L., Dahlberg, A.E., Gregory, S.T., Jogl, G.

Citation:

Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
To be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.25Å R work:0.226R free:0.27

NDB ID:

6FKR

PDB ID:

6FKR 

Release:

2018-03-28

Title:

Crystal structure of the dolphin proline-rich antimicrobial peptide Tur1A bound to the Thermus thermophilus 70S ribosome

Classification:

RIBOSOME

Authors:

Mardirossian, M., Perebaskine, N., Benincasa, M., Gambato, S., Hofmann, S., Huter, P., Muller, C., Hilpert, K., Innis, C.A., Tossi, A., Wilson, D.N.

Citation:

The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome.
Cell Chem Biol pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.189R free:0.251

NDB ID:

5ZEG

PDB ID:

5ZEG 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.177R free:0.215

NDB ID:

5ZEI

PDB ID:

5ZEI 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.2R free:0.25

NDB ID:

5ZEJ

PDB ID:

5ZEJ 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.5Å R work:0.205R free:0.228

NDB ID:

5ZEM

PDB ID:

5ZEM 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

X-RAY DIFFRACTION Resolution:3.103Å R work:0.255R free:0.283

NDB ID:

5N5C

PDB ID:

5N5C 

Release:

2018-03-14

Title:

NMR solution structure of the TSL2 RNA hairpin

Classification:

RNA

Authors:

Garcia-Lopez, A., Wacker, A., Tessaro, F., Jonker, H.R.A., Richter, C., Comte, A., Berntenis, N., Schmucki, R., Hatje, K., Sciarra, D., Konieczny, P., Fournet, G., Faustino, I., Orozco, M., Artero, R., Goekjian, P., Metzger, F., Ebeling, M., Joseph, B., Schwalbe, H., Scapozza, L.

Citation:

Rational targeting of RNA structure in SMN2 transcripts reverses Spinal Muscular Atrophy molecular phenotypes
To be published pp. - 0

Experiment:

SOLUTION NMR

NDB ID:

5N94

PDB ID:

5N94 

Release:

2018-03-14

Title:

Crystal Structure of Drosophila DHX36 helicase in complex with polyU

Classification:

HYDROLASE

Authors:

Chen, W.F., Rety, S., Guo, H.L., Dai, Y.X., Wu, W.Q., Liu, N.N., Auguin, D., Liu, Q.W., Hou, X.M., Dou, S.X., Xi, X.G.

Citation:

Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.
Structure 26 pp.403 - 415.e4 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.428Å R work:0.211R free:0.277

NDB ID:

5THE

PDB ID:

5THE 

Release:

2018-03-14

Title:

Crystal structure of the C-terminal lobe of a budding yeast Argonaute

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Dayeh, D.M., Kruithoff, B.C., Nakanishi, K.

Citation:

Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage.
J. Biol. Chem. 293 pp.6308 - 6325 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.097Å R work:0.157R free:0.205

NDB ID:

5YKI

PDB ID:

5YKI 

Release:

2018-03-14

Title:

Crystal structure of the engineered nine-repeat PUF domain in complex with cognate 9nt-RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhao, Y.Y., Mao, M.W., Zhang, W.J., Wang, J., Li, H.T., Yang, Y., Wang, Z., Wu, J.W.

Citation:

Expanding RNA binding specificity and affinity of engineered PUF domains.
Nucleic Acids Res. pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.25Å R work:0.196R free:0.236

NDB ID:

6CFJ

PDB ID:

6CFJ 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with histidyl-CAM and bound to mRNA and A-, P-, and E-site tRNAs at 2.8A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.268

NDB ID:

6CFK

PDB ID:

6CFK 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with D-histidyl-CAM and bound to protein Y (YfiA) at 2.7A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.205R free:0.252

NDB ID:

6CFL

PDB ID:

6CFL 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with lysyl-CAM and bound to protein Y (YfiA) at 2.6A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.208R free:0.251

NDB ID:

5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_03510.19 

Eq. Class Rep:

4V88

NDB ID:

5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_18586.20 

Eq. Class Rep:

5TBW

NDB ID:

5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_90506.20 

Eq. Class Rep:

5TBW

NDB ID:

5UZA

PDB ID:

5UZA 

Release:

2018-02-28

Title:

Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)

Classification:

RNA

Authors:

Liu, Y., Holmstrom, E., Yu, P., Tan, K., Zuo, X., Nesbitt, D.J., Sousa, R., Stagno, J.R., Wang, Y.X.

Citation:

Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.
Nat Protoc 13 pp.987 - 1005 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.22Å R work:0.215R free:0.25

Equivalence Class: 

NR_all_59689.4 

Eq. Class Rep:

4XNR

NDB ID:

5X70

PDB ID:

5X70 

Release:

2018-02-28

Title:

Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer

Classification:

TRANSFERASE/RNA

Authors:

Nakamichi, Y., Higashiura, A., Narita, H., Hagiwara, K., Uehara-Ichiki, T., Omura, T., Nakagawa, A.

Citation:

Crystal structure of capping enzyme from Rice dwarf virus
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.22R free:0.268

Equivalence Class: 

NR_all_10013.1 

Eq. Class Rep:

5X70

NDB ID:

6BJY

PDB ID:

6BJY 

Release:

2018-02-28

Title:

VSV Nucleocapsid with Polyamide Bound

Classification:

rna binding protein/rna

Authors:

Gumpper, R.H., Li, W., Castaneda, C.H., Scuderi, M.J., Bashkin, J.K., Luo, M.

Citation:

A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid.
J. Virol. 92 pp. - 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.46Å R work:0.265R free:0.31

Equivalence Class: 

NR_all_88517.3 

Eq. Class Rep:

4JNG

NDB ID:

6BLO

PDB ID:

6BLO 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i+1 position

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.401Å R work:0.202R free:0.227

Equivalence Class: 

NR_all_45110.1 

Eq. Class Rep:

6BLO

NDB ID:

6BLP

PDB ID:

6BLP 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.203Å R work:0.214R free:0.256

Equivalence Class: 

NR_all_45110.1 

Eq. Class Rep:

6BLO

NDB ID:

6BM2

PDB ID:

6BM2 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i-1 position

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.403Å R work:0.218R free:0.243

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

6BM4

PDB ID:

6BM4 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.951Å R work:0.234R free:0.26

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

6BQF

PDB ID:

6BQF 

Release:

2018-02-28

Title:

Pol II elongation complex with 'dT-AP' at i+1, i-1 position

Classification:

TRANSFERASE/TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.35Å R work:0.217R free:0.244

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

5N8L

PDB ID:

5N8L 

Release:

2018-02-21

Title:

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B)

Classification:

RNA BINDING PROTEIN

Authors:

Masliah, G., Maris, C., Konig, S.L., Yulikov, M., Aeschimann, F., Malinowska, A.L., Mabille, J., Weiler, J., Holla, A., Hunziker, J., Meisner-Kober, N., Schuler, B., Jeschke, G., Allain, F.H.

Citation:

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.
EMBO J. 37 pp. - 2018

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_25711.1 

Eq. Class Rep:

5N8L

NDB ID:

5N8M

PDB ID:

5N8M 

Release:

2018-02-21

Title:

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex A)

Classification:

RNA BINDING PROTEIN

Authors:

Masliah, G., Maris, C., Konig, S.L., Yulikov, M., Aeschimann, F., Malinowska, A.L., Mabille, J., Weiler, J., Holla, A., Hunziker, J., Meisner-Kober, N., Schuler, B., Jeschke, G., Allain, F.H.

Citation:

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.
EMBO J. 37 pp. - 2018

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_25711.1 

Eq. Class Rep:

5N8L

NDB ID:

5UX3

PDB ID:

5UX3 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.218R free:0.261

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

5UZ6

PDB ID:

5UZ6 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImp-oligo analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.221R free:0.266

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

5V0O

PDB ID:

5V0O 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG analogue bound

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.217R free:0.276

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

5V9Z

PDB ID:

5V9Z 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG analogue bound

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.51Å R work:0.218R free:0.281

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

5VCF

PDB ID:

5VCF 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.163R free:0.213

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

5VCI

PDB ID:

5VCI 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.162R free:0.212

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

5VGW

PDB ID:

5VGW 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

X-RAY DIFFRACTION Resolution:2.42Å R work:0.207R free:0.212

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

5WNP

PDB ID:

5WNP 

Release:

2018-02-21

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

RIBOSOME

Authors:

Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K.W., Wang, J., Petrov, A., Prabhakar, A., Rechavi, G., Dominissini, D., He, C., Ehrenberg, M., Puglisi, J.D.

Citation:

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Nat. Struct. Mol. Biol. 25 pp.208 - 216 2018

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.191R free:0.224

Equivalence Class: 

NR_all_65795.29 

Eq. Class Rep:

4LFB