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As of 14-Apr-2021 number of released structures: 11277
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 4207  Download results as an excel file       Gallery view

NDB ID:

 7A9W

PDB ID:

7A9W 

Release:

2021-04-07

Title:

Structure of yeast Rmd9p in complex with 20nt target RNA

Classification:

RNA BINDING PROTEIN

Authors:

Hillen, H.S., Markov, D.A., Ireneusz, W.D., Hofmann, K.B., Cowan, A.T., Jones, J.L., Temiakov, D., Cramer, P., Anikin, M.

Citation:

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs
Proc.Natl.Acad.Sci.USA pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.191R free:0.233

Equivalence Class: 

NR_all_38607.1 

Eq. Class Rep:

7A9W

NDB ID:

 7A9X

PDB ID:

7A9X 

Release:

2021-04-07

Title:

Structure of yeast Rmd9p in complex with 16nt target RNA

Classification:

RNA BINDING PROTEIN

Authors:

Hillen, H.S., Markov, D.A., Ireneusz, W.D., Hofmann, K.B., Cowan, A.T., Jones, J.L., Temiakov, D., Cramer, P., Anikin, M.

Citation:

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs
Proc.Natl.Acad.Sci.USA pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.45Å R work:0.198R free:0.232

Equivalence Class: 

NR_all_97545.1 

Eq. Class Rep:

7A9X

NDB ID:

 7C45

PDB ID:

7C45 

Release:

2021-04-07

Title:

The crystal structure of Trypanosoma brucei RNase D complex with RNA U12

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Gao, Y., Liu, H., Zhang, C., Su, S., Chen, Y., Chen, X., Li, Y., Shao, Z., Zhang, Y., Shao, Q., Li, J., Huang, Z., Ma, J., Gan, J.

Citation:

Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.
Nucleic Acids Res. 49 pp.568 - 583 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.769Å R work:0.192R free:0.221

Equivalence Class: 

NR_all_38094.1 

Eq. Class Rep:

7C45

NDB ID:

 7NBL

PDB ID:

7NBL 

Release:

2021-04-07

Title:

Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Classification:

DNA-RNA HYBRID

Authors:

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

Citation:

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_53230.1 

Eq. Class Rep:

7NEJ

NDB ID:

 7NEJ

PDB ID:

7NEJ 

Release:

2021-04-07

Title:

Solution structure of DNA:RNA hybrid duplex

Classification:

DNA-RNA HYBRID

Authors:

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

Citation:

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Chemistry pp. - 2021

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_53230.1 

Eq. Class Rep:

7NEJ

NDB ID:

 6WZR

PDB ID:

6WZR 

Release:

2021-03-24

Title:

Fusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA

Classification:

RNA

Authors:

Tran, B., Pichling, P., Tenney, L., Connelly, C.M., Moon, M.H., Ferre-D'Amare, A.R., Schneekloth Jr., J.S., Jones, C.P.

Citation:

Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.
Cell Chem Biol 27 pp.1241 - 1249.e4 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.2Å R work:0.206R free:0.248

Equivalence Class: 

NR_all_72776.1 

Eq. Class Rep:

5BTP

NDB ID:

 6WZS

PDB ID:

6WZS 

Release:

2021-03-24

Title:

Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA

Classification:

RNA

Authors:

Tran, B., Pichling, P., Tenney, L., Connelly, C.M., Moon, M.H., Ferre-D'Amare, A.R., Schneekloth Jr., J.S., Jones, C.P.

Citation:

Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.
Cell Chem Biol 27 pp.1241 - 1249.e4 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.23Å R work:0.223R free:0.258

Equivalence Class: 

NR_all_72776.1 

Eq. Class Rep:

5BTP

NDB ID:

 6M6R

PDB ID:

6M6R 

Release:

2021-03-17

Title:

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 8-mer ssRNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, K., Zheng, J., Wirawan, M., Xiong, Z., Fedorova, O., Griffin, P., Plyle, A., Luo, D.

Citation:

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.89Å R work:0.177R free:0.221

Equivalence Class: 

NR_all_71389.1 

Eq. Class Rep:

6M6R

NDB ID:

 6M6S

PDB ID:

6M6S 

Release:

2021-03-17

Title:

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain with 5'-ppp 12-mer dsRNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, K., Zheng, J., Wirawan, M., Xiong, Z., Fedorova, O., Griffin, P., Plyle, A., Luo, D.

Citation:

Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal domain
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.6Å R work:0.169R free:0.198

Equivalence Class: 

NR_all_37536.1 

Eq. Class Rep:

6M6S

NDB ID:

 6M75

PDB ID:

6M75 

Release:

2021-03-17

Title:

C-Myc DNA binding protein complex

Classification:

DNA BINDING PROTEIN/DNA

Authors:

Aggarwal, P., Bhavesh, N.S.

Citation:

c-Myc DNA binding protein complex
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.57Å R work:0.211R free:0.235

NDB ID:

 7DIC

PDB ID:

7DIC 

Release:

2021-03-17

Title:

Mycoplasma genitalium RNase R in complex with single-stranded RNA

Classification:

HYDROLASE/RNA

Authors:

Abula, A., Li, X., Quan, X., Yang, T., Liu, Y., Guo, H., Li, T., Ji, X.

Citation:

Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.242Å R work:0.215R free:0.261

Equivalence Class: 

NR_all_35047.1 

Eq. Class Rep:

7DIC

NDB ID:

 7DID

PDB ID:

7DID 

Release:

2021-03-17

Title:

Mycoplasma genitalium RNase R in complex with ribose methylated single-stranded RNA

Classification:

HYDROLASE/RNA

Authors:

Abula, A., Li, X., Quan, X., Yang, T., Liu, Y., Guo, H., Li, T., Ji, X.

Citation:

Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.188R free:0.221

Equivalence Class: 

NR_all_64918.9 

Eq. Class Rep:

6SCE

NDB ID:

 7DOL

PDB ID:

7DOL 

Release:

2021-03-17

Title:

Mycoplasma genitalium RNase R in complex with double-stranded RNA

Classification:

HYDROLASE/RNA

Authors:

Abula, A., Li, X., Quan, X., Yang, T., Liu, Y., Guo, H., Li, T., Ji, X.

Citation:

Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Nucleic Acids Res. pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.002Å R work:0.22R free:0.242

Equivalence Class: 

NR_all_79034.1 

Eq. Class Rep:

7DOL

NDB ID:

 7LVA

PDB ID:

7LVA 

Release:

2021-03-17

Title:

Solution structure of the HIV-1 PBS-segment

Classification:

RNA

Authors:

Song, Z., Heng, X.

Citation:

Structure of the HIV-1 PBS-segment is conserved for viral infectivity
To Be Published pp. - 0

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_81372.1 

Eq. Class Rep:

7LVA

NDB ID:

 6W11

PDB ID:

6W11 

Release:

2021-03-10

Title:

The structure of Sulfolobus solfataricus Csa3 in complex with cyclic tetraadenylate (cA4)

Classification:

TRANSCRIPTION

Authors:

Charbonneau, A.A., Gauvin, C.C., Lawrence, C.M.

Citation:

The structure of Sulfolobus solfataricus Csa3 in complex with cyclic tetraadenylate (cA4)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.46Å R work:0.202R free:0.242

Equivalence Class: 

NR_all_64918.9 

Eq. Class Rep:

6SCE

NDB ID:

 7A3Y

PDB ID:

7A3Y 

Release:

2021-03-10

Title:

RNA duplex with a cytosine bulge in complex with berberine

Classification:

RNA

Authors:

Podbevsek, P., Plavec, J.

Citation:

Interaction between berberine and RNA for the exploration of phytochemicals role
Nucleic Acids Res. pp. - 2021

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_22270.1 

Eq. Class Rep:

7A3Y

NDB ID:

 6WLH

PDB ID:

6WLH 

Release:

2021-03-03

Title:

RNA complex of WT1 zinc finger transcription factor

Classification:

TRANSCRIPTION

Authors:

Nishikawa, T., Wojciak, J.M., Dyson, H.J., Wright, P.E.

Citation:

RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1.
Biochemistry 59 pp.3889 - 3901 2020

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_53524.1 

Eq. Class Rep:

6WLH

NDB ID:

 7BDV

PDB ID:

7BDV 

Release:

2021-03-03

Title:

Structure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)

Classification:

DNA BINDING PROTEIN

Authors:

Zhu, W., McQuarrie, S., Gruschow, S., McMahon, S.A., Graham, S., Gloster, T.M., White, M.F.

Citation:

The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence.
Nucleic Acids Res. 49 pp.2777 - 2789 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.02Å R work:0.24R free:0.29

Equivalence Class: 

NR_all_64918.9 

Eq. Class Rep:

6SCE

NDB ID:

 7BPV

PDB ID:

7BPV 

Release:

2021-03-03

Title:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid duplex structure

Classification:

DNA-RNA HYBRID

Authors:

Wang, S.C., Satange, R.B., Hou, M.H.

Citation:

r(GUGGGCCGAC)/d(GTCGGCCCAC) hybrid structure
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.781Å R work:0.217R free:0.237

Equivalence Class: 

NR_all_15457.1 

Eq. Class Rep:

7BPV

NDB ID:

 7K9D

PDB ID:

7K9D 

Release:

2021-03-03

Title:

Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal form I)

Classification:

RNA-BINDING PROTEIN/RNA

Authors:

Yang, Y., Harris, K.A., Widner, D.L., Breaker, R.R.

Citation:

Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.098Å R work:0.161R free:0.198

Equivalence Class: 

NR_all_72196.1 

Eq. Class Rep:

7KKV

NDB ID:

 7K9E

PDB ID:

7K9E 

Release:

2021-03-03

Title:

Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (crystal form II)

Classification:

RNA-BINDING PROTEIN/RNA

Authors:

Yang, Y., Harris, K.A., Widner, D.L., Breaker, R.R.

Citation:

Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.171R free:0.203

Equivalence Class: 

NR_all_72196.1 

Eq. Class Rep:

7KKV

NDB ID:

 7KD1

PDB ID:

7KD1 

Release:

2021-03-03

Title:

Apo structure of the THF riboswitch aptamer domain

Classification:

RNA

Authors:

Wilt, H.M., Yu, P., Tan, K., Wang, Y.X., Stagno, J.R.

Citation:

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation.
J.Struct.Biol. 213 pp.107703 - 107703 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.204R free:0.225

Equivalence Class: 

NR_all_78797.5 

Eq. Class Rep:

4LVW

NDB ID:

 7KKV

PDB ID:

7KKV 

Release:

2021-03-03

Title:

Crystal structure of Bacillus halodurans OapB in complex with its OLE RNA target (native, crystal form I)

Classification:

RNA-BINDING PROTEIN/RNA

Authors:

Yang, Y., Harris, K.A., Widner, D.L., Breaker, R.R.

Citation:

Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex.
Proc.Natl.Acad.Sci.USA 118 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.169R free:0.187

Equivalence Class: 

NR_all_72196.1 

Eq. Class Rep:

7KKV

NDB ID:

 6Y0T

PDB ID:

6Y0T 

Release:

2021-02-17

Title:

Sarcin Ricin Loop, mutant C2666A U2653G C2667A

Classification:

RNA

Authors:

Ennifar, E., Westhof, E.

Citation:

Sarcin Ricin Loop, mutant C2666A U2653G C2667A
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.393Å R work:0.165R free:0.202

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 6Y0Y

PDB ID:

6Y0Y 

Release:

2021-02-17

Title:

Sarcin Ricin Loop, mutant C2666U

Classification:

RNA

Authors:

Ennifar, E., Westhof, E.

Citation:

Sarcin Ricin Loop, mutant C2666U
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:0.95Å R work:0.125R free:0.138

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 6VRD

PDB ID:

6VRD 

Release:

2021-02-10

Title:

Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level

Classification:

HYDROLASE/RNA

Authors:

Cho, Y.J., Butler, D.

Citation:

Crystal structure of RNase H/RNA/PS-ASO complex at an atomic level
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.299Å R work:0.189R free:0.228

Equivalence Class: 

NR_all_79785.1 

Eq. Class Rep:

6VRD

NDB ID:

 6XUS

PDB ID:

6XUS 

Release:

2021-02-03

Title:

RNA dodecamer with a 6-hydrazino-2-aminopurine modified base

Classification:

RNA

Authors:

Gasser, C., Delazer, I., Pascher, K., Brillet, K., Klotz, S., Himmelsoss, M., Ennifar, E., Rieder, D., Lusser, A., Micura, R.

Citation:

RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.1Å R work:0.153R free:0.173

Equivalence Class: 

NR_all_17726.3 

Eq. Class Rep:

6XUS

NDB ID:

 7KL3

PDB ID:

7KL3 

Release:

2021-02-03

Title:

The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to RNA oligomer AG*CAUC (*uncleaveable bond, -UC disordered)

Classification:

VIRAL PROTEIN/RNA

Authors:

Kumar, G., Cuypers, M., Webby, R.R., Webb, T.R., White, S.W.

Citation:

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Nucleic Acids Res. 49 pp.1609 - 1618 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.99Å R work:0.177R free:0.209

Equivalence Class: 

NR_all_68310.1 

Eq. Class Rep:

7KL3

NDB ID:

 6LT7

PDB ID:

6LT7 

Release:

2021-01-27

Title:

Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP

Classification:

HYDROLASE/RNA

Authors:

Yin, C., Bai, G., Zhang, Y., Huang, J.

Citation:

Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP.
J.Struct.Biol. 213 pp.107704 - 107704 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.191R free:0.238

Equivalence Class: 

NR_all_25335.1 

Eq. Class Rep:

6LT7

NDB ID:

 7JNH

PDB ID:

7JNH 

Release:

2021-01-20

Title:

Crystal structure of a double-ENE RNA stability element in complex with a 28-mer poly(A) RNA

Classification:

RNA

Authors:

Torabi, S.F., Vaidya, A.T., Tycowski, K.T., DeGregorio, S.J., Wang, J., Shu, M.D., Steitz, T.A., Steitz, J.A.

Citation:

RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction.
Science 371 pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.89Å R work:0.184R free:0.225

Equivalence Class: 

NR_all_91654.1 

Eq. Class Rep:

7JNH

NDB ID:

 6XKI

PDB ID:

6XKI 

Release:

2021-01-06

Title:

Crystal structure of eIF4A-I in complex with RNA bound to des-MePateA, a pateamine A analog

Classification:

TRANSLATION/RNA/INHIBITOR

Authors:

Naineni, S.K., Liang, J., Hull, K., Cencic, R., Zhu, M., Northcote, P., Teesdale-Spittle, P., Romo, D., Nagar, B., Pelletier, J.

Citation:

Functional mimicry revealed by the crystal structure of an eIF4A:RNA complex bound to the interfacial inhibitor, desmethyl pateamine A.
Cell Chem Biol pp. - 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.87Å R work:0.221R free:0.262

Equivalence Class: 

NR_all_14757.1 

Eq. Class Rep:

5ZC9

NDB ID:

 7L6R

PDB ID:

7L6R 

Release:

2021-01-06

Title:

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and Manganese (Mn).

Classification:

VIRAL PROTEIN/RNA

Authors:

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Citation:

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and Manganese (Mn).
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.98Å R work:0.15R free:0.166

Equivalence Class: 

NR_all_11762.2 

Eq. Class Rep:

7L6T

NDB ID:

 7L6T

PDB ID:

7L6T 

Release:

2021-01-06

Title:

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.

Classification:

VIRAL PROTEIN/RNA

Authors:

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Kiryukhina, O., Brunzelle, J.S., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Citation:

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.78Å R work:0.14R free:0.161

Equivalence Class: 

NR_all_11762.2 

Eq. Class Rep:

7L6T

NDB ID:

 6VAR

PDB ID:

6VAR 

Release:

2020-12-30

Title:

61 nt human Hepatitis B virus epsilon pre-genomic RNA

Classification:

RNA

Authors:

LeBlanc, R.M., Kasprzak, W.K., Longhini, A.P., Abulwerdi, F., Ginocchio, S., Shields, B., Nyman, J., Svirydava, M., Del Vecchio, C., Ivanic, J., Schneekloth, J.S., Dayie, T.K., Shapiro, B.A., Le Grice, S.F.J.

Citation:

Structural insights of the conserved 'priming loop' of Hepatitis B virus pre-genomic RNA and its therapeutic potential.
To be published pp. - 0

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_39208.1 

Eq. Class Rep:

6VAR

NDB ID:

 6WXX

PDB ID:

6WXX 

Release:

2020-12-30

Title:

crystal structure of cA4-activated Card1

Classification:

DNA BINDING PROTEIN/RNA

Authors:

Rostol, J.T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R., Patel, D.J., Marraffini, L.A.

Citation:

The Card1 nuclease provides defence during type III CRISPR immunity.
Nature 590 pp.624 - 629 2021

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.203R free:0.237

Equivalence Class: 

NR_all_64918.9 

Eq. Class Rep:

6SCE

NDB ID:

 6WXY

PDB ID:

6WXY 

Release:

2020-12-30

Title:

crystal structure of cA6-bound Card1

Classification:

DNA BINDING PROTEIN/RNA

Authors:

Rostol, J.T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R., Patel, D.J., Marraffini, L.A.

Citation:

The Card1 nuclease provides defence during type III CRISPR immunity.
Nature 590 pp.624 - 629 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.206R free:0.244

Equivalence Class: 

NR_all_00429.1 

Eq. Class Rep:

6WXY

NDB ID:

 6XL1

PDB ID:

6XL1 

Release:

2020-12-30

Title:

crystal structure of cA4-activated Card1(D294N)

Classification:

DNA BINDING PROTEIN/RNA

Authors:

Rostol, J.T., Xie, W., Kuryavyi, V., Maguin, P., Kao, K., Froom, R., Patel, D.J., Marraffini, L.A.

Citation:

The Card1 nuclease provides defence during type III CRISPR immunity.
Nature 590 pp.624 - 629 2021

Experiment:

 X-RAY DIFFRACTION Resolution:1.95Å R work:0.177R free:0.201

Equivalence Class: 

NR_all_64918.9 

Eq. Class Rep:

6SCE

NDB ID:

 6Y3G

PDB ID:

6Y3G 

Release:

2020-12-30

Title:

Crystal structure of phenylalanine tRNA from Escherichia coli

Classification:

RNA

Authors:

Bourgeois, G., Seguin, J., Babin, M., Gondry, M., Mechulam, Y., Schmitt, E.

Citation:

Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Rna 26 pp.1589 - 1602 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.215R free:0.236

Equivalence Class: 

NR_all_19951.44 

Eq. Class Rep:

4YCO

NDB ID:

 6Y4B

PDB ID:

6Y4B 

Release:

2020-12-30

Title:

Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe

Classification:

RNA BINDING PROTEIN

Authors:

Bourgeois, G., Seguin, J., Babin, M., Gondry, M., Mechulam, Y., Schmitt, E.

Citation:

Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Rna 26 pp.1589 - 1602 2020

Experiment:

 X-RAY DIFFRACTION Resolution:5.0Å R work:0.303R free:0.315

Equivalence Class: 

NR_all_19951.44 

Eq. Class Rep:

4YCO

NDB ID:

 6XHV

PDB ID:

6XHV 

Release:

2020-12-23

Title:

Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution

Classification:

RIBOSOME

Authors:

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

Citation:

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.
Nat.Chem.Biol. 17 pp.412 - 420 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.4Å R work:0.237R free:0.285

Equivalence Class: 

NR_all_65795.58 

Eq. Class Rep:

4LFB

NDB ID:

 6XHW

PDB ID:

6XHW 

Release:

2020-12-23

Title:

Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution

Classification:

RIBOSOME

Authors:

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

Citation:

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.
Nat.Chem.Biol. 17 pp.412 - 420 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.232R free:0.281

Equivalence Class: 

NR_all_65795.58 

Eq. Class Rep:

4LFB

NDB ID:

 6XHX

PDB ID:

6XHX 

Release:

2020-12-23

Title:

Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with erythromycin and protein Y (YfiA) at 2.55A resolution

Classification:

RIBOSOME

Authors:

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

Citation:

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.
Nat.Chem.Biol. 17 pp.412 - 420 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.55Å R work:0.221R free:0.272

Equivalence Class: 

NR_all_65795.58 

Eq. Class Rep:

4LFB

NDB ID:

 6XHY

PDB ID:

6XHY 

Release:

2020-12-23

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with telithromycin, mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.60A resolution

Classification:

RIBOSOME

Authors:

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

Citation:

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.
Nat.Chem.Biol. 17 pp.412 - 420 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.216R free:0.265

Equivalence Class: 

NR_all_65795.58 

Eq. Class Rep:

4LFB

NDB ID:

 6YYM

PDB ID:

6YYM 

Release:

2020-12-23

Title:

Structure of S. pombe Mei2 RRM3 domain bound to RNA

Classification:

RNA BINDING PROTEIN

Authors:

Andric, V., Nevers, A., Hazra, D., Auxilien, S., Menant, A., Graille, M., Palancade, B., Rougemaille, M.

Citation:

A scaffold lncRNA shapes the mitosis to meiosis switch.
Nat Commun 12 pp.770 - 770 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.63Å R work:0.223R free:0.298

Equivalence Class: 

NR_all_04435.1 

Eq. Class Rep:

6YYM

NDB ID:

 7JJD

PDB ID:

7JJD 

Release:

2020-12-23

Title:

Sarcin-ricin loop with guanosine monothiophosphate residue.

Classification:

RNA

Authors:

Pallan, P.S., Lybrand, T.P., Schlegel, M.K., Harp, J.M., Jahns, H., Manoharan, M., Egli, M.

Citation:

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Biochemistry 59 pp.4627 - 4637 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.21Å R work:0.172R free:0.238

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 7JJE

PDB ID:

7JJE 

Release:

2020-12-23

Title:

Sarcin-ricin loop with guanosine dithiophosphate residue.

Classification:

RNA

Authors:

Pallan, P.S., Lybrand, T.P., Schlegel, M.K., Harp, J.M., Jahns, H., Manoharan, M., Egli, M.

Citation:

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Biochemistry 59 pp.4627 - 4637 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.25Å R work:0.11R free:0.147

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 7JJF

PDB ID:

7JJF 

Release:

2020-12-23

Title:

Sarcin-ricin loop with modified residue.

Classification:

DNA-RNA HYBRID

Authors:

Pallan, P.S., Lybrand, T.P., Schlegel, M.K., Harp, J.M., Jahns, H., Manoharan, M., Egli, M.

Citation:

Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Biochemistry 59 pp.4627 - 4637 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.2Å R work:0.177R free:0.214

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 6ZXZ

PDB ID:

6ZXZ 

Release:

2020-12-16

Title:

Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification

Classification:

RNA

Authors:

Himmelstoss, M., Erharter, K., Renard, E., Ennifar, E., Kreutz, C., Micura, R.

Citation:

2'-O-Trifluoromethylated RNA - A powerful modification for RNA chemistry and NMR spectroscopy
Chem Sci pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.44Å R work:0.21R free:0.231

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 6ZYB

PDB ID:

6ZYB 

Release:

2020-12-16

Title:

Sarcin-Ricin Loop RNA from Ecoli with a C2667-2'-OCF3 modification

Classification:

RNA

Authors:

Himmelstoss, M., Erharter, K., Renard, E., Ennifar, E., Kreutz, C., Micura, R.

Citation:

2'-O-Trifluoromethylated RNA - A powerful modification for RNA chemistry and NMR spectroscopy
Chem Sci pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:0.9Å R work:0.13R free:0.149

Equivalence Class: 

NR_all_94729.6 

Eq. Class Rep:

4NLF

NDB ID:

 6U7Y

PDB ID:

6U7Y 

Release:

2020-12-09

Title:

RNA hairpin structure containing one TNA nucleotide as template

Classification:

RNA

Authors:

Zhang, W., Kim, S.C., Tam, C.P., Lelyveld, V.S., Bala, S., Chaput, J.C., Szostak, J.W.

Citation:

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.
Nucleic Acids Res. 49 pp.646 - 656 2021

Experiment:

 X-RAY DIFFRACTION Resolution:2.95Å R work:0.181R free:0.256

Equivalence Class: 

NR_all_95948.1 

Eq. Class Rep:

5VCI

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