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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 5252  Download results as an excel file       Gallery view

NDB ID:

 6K84

PDB ID:

6K84 

Release:

2020-04-01

Title:

Structure of anti-prion RNA aptamer

Classification:

RNA

Authors:

Mashima, T., Lee, J.H., Kamatari, Y.O., Hayashi, T., Nagata, T., Nishikawa, F., Nishikawa, S., Kinoshita, M., Kuwata, K., Katahira, M.

Citation:

Development and structural determination of an anti-PrPCaptamer that blocks pathological conformational conversion of prion protein.
Sci Rep 10 pp.4934 - 4934 2020

Experiment:

 SOLUTION NMR

NDB ID:

 6KON

PDB ID:

6KON 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.0Å R work:0.22R free:0.27

Equivalence Class: 

NR_all_54899.1 

Eq. Class Rep:

6KQF

NDB ID:

 6KOO

PDB ID:

6KOO 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 7 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.206R free:0.247

Equivalence Class: 

NR_all_90383.1 

Eq. Class Rep:

6KOO

NDB ID:

 6KOP

PDB ID:

6KOP 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 9 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.303Å R work:0.217R free:0.254

Equivalence Class: 

NR_all_38519.1 

Eq. Class Rep:

6KOP

NDB ID:

 6KOQ

PDB ID:

6KOQ 

Release:

2020-03-11

Title:

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 10 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.353Å R work:0.22R free:0.26

Equivalence Class: 

NR_all_90532.1 

Eq. Class Rep:

6KOQ

NDB ID:

 6KQD

PDB ID:

6KQD 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.206R free:0.249

Equivalence Class: 

NR_all_79699.1 

Eq. Class Rep:

6KQD

NDB ID:

 6KQE

PDB ID:

6KQE 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 4 nt

Classification:

TRANSLATION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.217R free:0.258

Equivalence Class: 

NR_all_90795.5 

Eq. Class Rep:

6KQE

NDB ID:

 6KQF

PDB ID:

6KQF 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.45Å R work:0.198R free:0.229

Equivalence Class: 

NR_all_54899.1 

Eq. Class Rep:

6KQF

NDB ID:

 6KQG

PDB ID:

6KQG 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 6 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.783Å R work:0.204R free:0.247

Equivalence Class: 

NR_all_68486.1 

Eq. Class Rep:

6JCY

NDB ID:

 6KQH

PDB ID:

6KQH 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 7 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.18Å R work:0.202R free:0.246

Equivalence Class: 

NR_all_90383.1 

Eq. Class Rep:

6KOO

NDB ID:

 6KQL

PDB ID:

6KQL 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 4 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.89Å R work:0.207R free:0.246

Equivalence Class: 

NR_all_89748.1 

Eq. Class Rep:

6KQL

NDB ID:

 6KQM

PDB ID:

6KQM 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 5 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.197Å R work:0.205R free:0.251

Equivalence Class: 

NR_all_20925.1 

Eq. Class Rep:

6KQM

NDB ID:

 6KQN

PDB ID:

6KQN 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 6 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.489Å R work:0.213R free:0.258

Equivalence Class: 

NR_all_21296.1 

Eq. Class Rep:

6KQN

NDB ID:

 6L74

PDB ID:

6L74 

Release:

2020-03-11

Title:

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 2 nt

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.12Å R work:0.19R free:0.235

Equivalence Class: 

NR_all_04288.3 

Eq. Class Rep:

6N6E

NDB ID:

 6TYE

PDB ID:

6TYE 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.79Å R work:0.234R free:0.279

Equivalence Class: 

NR_all_54899.1 

Eq. Class Rep:

6KQF

NDB ID:

 6TYF

PDB ID:

6TYF 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.8Å R work:0.256R free:0.299

Equivalence Class: 

NR_all_68486.1 

Eq. Class Rep:

6JCY

NDB ID:

 6TYG

PDB ID:

6TYG 

Release:

2020-03-11

Title:

Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer

Classification:

TRANSCRIPTION

Authors:

Li, L., Molodtsov, V., Lin, W., Ebright, R.H., Zhang, Y.

Citation:

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Proc.Natl.Acad.Sci.USA 117 pp.5801 - 5809 2020

Experiment:

 X-RAY DIFFRACTION Resolution:3.5Å R work:0.246R free:0.293

Equivalence Class: 

NR_all_38519.1 

Eq. Class Rep:

6KOP

NDB ID:

 6JJH

PDB ID:

6JJH 

Release:

2020-02-26

Title:

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4

Classification:

RNA

Authors:

Zhang, Y.S., EI Omari, K., Duman, R., Wagner, A., Parkinson, G.N., Wei, D.G.

Citation:

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:1.74Å R work:0.239R free:0.291

Equivalence Class: 

NR_all_07071.1 

Eq. Class Rep:

6JJH

NDB ID:

 6JJI

PDB ID:

6JJI 

Release:

2020-02-26

Title:

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1)

Classification:

RNA

Authors:

Zhang, Y.S., Parkinson, G.N., Wei, D.G.

Citation:

Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.192R free:0.249

Equivalence Class: 

NR_all_28332.1 

Eq. Class Rep:

6JJI

NDB ID:

 6OWL

PDB ID:

6OWL 

Release:

2020-02-26

Title:

RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP

Classification:

RNA

Authors:

Kim, S.C., Zhou, L., Zhang, W., O'Flaherty, D.K., Rondo-Brovetto, V., Szostak, J.W.

Citation:

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.
J.Am.Chem.Soc. 142 pp.2317 - 2326 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.237R free:0.317

Equivalence Class: 

NR_all_01949.2 

Eq. Class Rep:

5UED

NDB ID:

 6OWL

PDB ID:

6OWL 

Release:

2020-02-26

Title:

RNA oligonucleotides with 3'-arabino guanosine co-crystallized with GMP

Classification:

RNA

Authors:

Kim, S.C., Zhou, L., Zhang, W., O'Flaherty, D.K., Rondo-Brovetto, V., Szostak, J.W.

Citation:

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.
J.Am.Chem.Soc. 142 pp.2317 - 2326 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.237R free:0.317

Equivalence Class: 

NR_all_89612.8 

Eq. Class Rep:

6N6I

NDB ID:

 6KR6

PDB ID:

6KR6 

Release:

2020-02-19

Title:

Crystal structure of Drosophila Piwi

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Yamaguchi, S., Oe, A., Nishida, K.M., Yamashita, K., Kajiya, A., Hirano, S., Matsumoto, N., Dohmae, N., Ishitani, R., Saito, K., Siomi, H., Nishimasu, H., Siomi, M.C., Nureki, O.

Citation:

Crystal structure of Drosophila Piwi.
Nat Commun 11 pp.858 - 858 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.9Å R work:0.239R free:0.258

Equivalence Class: 

NR_all_67557.1 

Eq. Class Rep:

6KR6

NDB ID:

 6SCE

PDB ID:

6SCE 

Release:

2020-02-19

Title:

Structure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate

Classification:

DNA

Authors:

McMahon, S.A., Zhu, W., Graham, S., Rambo, R., White, M.F., Gloster, T.M.

Citation:

Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate.
Nat Commun 11 pp.500 - 500 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.83Å R work:0.176R free:0.209

Equivalence Class: 

NR_all_64918.4 

Eq. Class Rep:

6SCE

NDB ID:

 6XUR

PDB ID:

6XUR 

Release:

2020-02-19

Title:

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

Classification:

RNA

Authors:

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

Citation:

Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL).
Angew.Chem.Int.Ed.Engl. pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.1Å R work:0.153R free:0.18

Equivalence Class: 

NR_all_17726.2 

Eq. Class Rep:

6XUR

NDB ID:

 6TPH

PDB ID:

6TPH 

Release:

2020-02-12

Title:

Structure of a protein-RNA complex by ssNMR

Classification:

RNA

Authors:

Ahmed, M., Marchanka, A., Carlomagno, T.

Citation:

Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy.
Angew.Chem.Int.Ed.Engl. pp. - 2020

Experiment:

 SOLID-STATE NMR

Equivalence Class: 

NR_all_94548.1 

Eq. Class Rep:

2N0R

NDB ID:

 6KTC

PDB ID:

6KTC 

Release:

2020-02-05

Title:

Crystal structure of YBX1 CSD with m5C RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zou, F., Tu, R., Duan, B., Yang, Z., Ping, Z., Song, X., Chen, S., Price, A., Li, H., Scott, A., Perera, A., Li, S., Xie, T.

Citation:

DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.
Proc.Natl.Acad.Sci.USA 117 pp.3603 - 3609 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.008Å R work:0.237R free:0.273

Equivalence Class: 

NR_all_78647.1 

Eq. Class Rep:

6KUG

NDB ID:

 6KUG

PDB ID:

6KUG 

Release:

2020-02-05

Title:

Crystal structure of YBX1 CSD with RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zou, F., Tu, R., Duan, B., Yang, Z., Ping, Z., Song, X., Chen, S., Price, A., Li, H., Scott, A., Perera, A., Li, S., Xie, T.

Citation:

DrosophilaYBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs.
Proc.Natl.Acad.Sci.USA 117 pp.3603 - 3609 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.4Å R work:0.178R free:0.212

Equivalence Class: 

NR_all_78647.1 

Eq. Class Rep:

6KUG

NDB ID:

 6SY4

PDB ID:

6SY4 

Release:

2020-02-05

Title:

TetR in complex with the TetR-binding RNA-aptamer K1

Classification:

DNA BINDING PROTEIN

Authors:

Grau, F.C., Jaeger, J., Groher, F., Suess, B., Muller, Y.A.

Citation:

The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex.
Nucleic Acids Res. pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.695Å R work:0.201R free:0.246

Equivalence Class: 

NR_all_00338.1 

Eq. Class Rep:

6SY4

NDB ID:

 6SY6

PDB ID:

6SY6 

Release:

2020-02-05

Title:

TetR in complex with the TetR-binding RNA-aptamer K2

Classification:

DNA BINDING PROTEIN

Authors:

Grau, F.C., Jaeger, J., Groher, F., Suess, B., Muller, Y.A.

Citation:

The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex.
Nucleic Acids Res. pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.9Å R work:0.247R free:0.288

Equivalence Class: 

NR_all_65081.1 

Eq. Class Rep:

6SY6

NDB ID:

 6JBF

PDB ID:

6JBF 

Release:

2020-01-29

Title:

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)

Classification:

RNA/ANTIBIOTIC

Authors:

Kondo, J., Hanessian, S., Kanazawa, H.

Citation:

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.153R free:0.229

Equivalence Class: 

NR_all_71199.2 

Eq. Class Rep:

5Z1I

NDB ID:

 6JBG

PDB ID:

6JBG 

Release:

2020-01-29

Title:

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)

Classification:

RNA/ANTIBIOTIC

Authors:

Kondo, J., Hanessian, S., Kanazawa, H.

Citation:

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.16R free:0.225

Equivalence Class: 

NR_all_71199.2 

Eq. Class Rep:

5Z1I

NDB ID:

 6SDW

PDB ID:

6SDW 

Release:

2020-01-15

Title:

Solution structure of Staufen1 dsRBD3+4 - hARF1 SBS dsRNA complex.

Classification:

RNA BINDING PROTEIN

Authors:

Yadav, D.K., Zigackova, D., Zlobina, M., Klumpler, T., Beaumont, C., Kubickova, M., Vanacova, S., Lukavsky, P.J.

Citation:

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
Nucleic Acids Res. 48 pp.2091 - 2106 2020

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_54922.1 

Eq. Class Rep:

6SDW

NDB ID:

 6SDY

PDB ID:

6SDY 

Release:

2020-01-15

Title:

Solution structure of Staufen1 dsRBD4 - hARF1 SBS dsRNA complex.

Classification:

RNA BINDING PROTEIN

Authors:

Yadav, D.K., Zigackova, D., Zlobina, M., Klumpler, T., Beaumont, C., Kubickova, M., Vanacova, S., Lukavsky, P.J.

Citation:

Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
Nucleic Acids Res. 48 pp.2091 - 2106 2020

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_94180.1 

Eq. Class Rep:

6SDY

NDB ID:

 6PRV

PDB ID:

6PRV 

Release:

2020-01-08

Title:

58nt RNA L11-binding domain from E. coli 23S rRNA

Classification:

RNA

Authors:

Welty, R., Rau, M., Pabit, S., Dunstan, M.S., Conn, G.L., Pollack, L., Hall, K.B.

Citation:

Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.
J.Mol.Biol. 432 pp.991 - 1007 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.71Å R work:0.203R free:0.259

Equivalence Class: 

NR_all_25376.1 

Eq. Class Rep:

6PRV

NDB ID:

 6JVX

PDB ID:

6JVX 

Release:

2020-01-01

Title:

Crystal structure of RBM38 in complex with RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Qian, K., Li, M., Wang, J., Zhang, M., Wang, M.

Citation:

Structural basis for mRNA recognition by human RBM38.
Biochem.J. 477 pp.161 - 172 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.301Å R work:0.177R free:0.22

Equivalence Class: 

NR_all_97043.1 

Eq. Class Rep:

6JVX

NDB ID:

 6L1W

PDB ID:

6L1W 

Release:

2020-01-01

Title:

Zinc-finger Antiviral Protein (ZAP) bound to RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Luo, X., Wang, X., Gao, Y., Zhu, J., Liu, S., Gao, G., Gao, P.

Citation:

Molecular Mechanism of RNA Recognition by Zinc-Finger Antiviral Protein.
Cell Rep 30 pp.46 - 52.e4 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.194Å R work:0.205R free:0.245

Equivalence Class: 

NR_all_28499.1 

Eq. Class Rep:

6L1W

NDB ID:

 6LAS

PDB ID:

6LAS 

Release:

2020-01-01

Title:

the wildtype SAM-VI riboswitch bound to SAM

Classification:

RNA

Authors:

Sun, A., Gasser, C., Li, F., Chen, H., Mair, S., Krasheninina, O., Micura, R., Ren, A.

Citation:

SAM-VI riboswitch structure and signature for ligand discrimination.
Nat Commun 10 pp.5728 - 5728 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.708Å R work:0.206R free:0.243

Equivalence Class: 

NR_all_47836.1 

Eq. Class Rep:

6LAX

NDB ID:

 6LAU

PDB ID:

6LAU 

Release:

2020-01-01

Title:

the wildtype SAM-VI riboswitch bound to SAH

Classification:

RNA

Authors:

Sun, A., Gasser, C., Li, F., Chen, H., Mair, S., Krasheninina, O., Micura, R., Ren, A.

Citation:

SAM-VI riboswitch structure and signature for ligand discrimination.
Nat Commun 10 pp.5728 - 5728 2019

Experiment:

 X-RAY DIFFRACTION Resolution:3.109Å R work:0.19R free:0.251

Equivalence Class: 

NR_all_47836.1 

Eq. Class Rep:

6LAX

NDB ID:

 6LAX

PDB ID:

6LAX 

Release:

2020-01-01

Title:

the mutant SAM-VI riboswitch (U6C) bound to SAM

Classification:

RNA

Authors:

Sun, A., Gasser, C., Li, F., Chen, H., Mair, S., Krasheninina, O., Micura, R., Ren, A.

Citation:

SAM-VI riboswitch structure and signature for ligand discrimination.
Nat Commun 10 pp.5728 - 5728 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.188R free:0.239

Equivalence Class: 

NR_all_47836.1 

Eq. Class Rep:

6LAX

NDB ID:

 6LAZ

PDB ID:

6LAZ 

Release:

2020-01-01

Title:

the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1

Classification:

RNA

Authors:

Sun, A., Gasser, C., Li, F., Chen, H., Mair, S., Krasheninina, O., Micura, R., Ren, A.

Citation:

SAM-VI riboswitch structure and signature for ligand discrimination.
Nat Commun 10 pp.5728 - 5728 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.76Å R work:0.187R free:0.223

Equivalence Class: 

NR_all_47836.1 

Eq. Class Rep:

6LAX

NDB ID:

 6LLB

PDB ID:

6LLB 

Release:

2020-01-01

Title:

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, D.F., Hou, Y.J., Guo, L.

Citation:

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.187R free:0.224

Equivalence Class: 

NR_all_25498.1 

Eq. Class Rep:

6LLB

NDB ID:

 6LLB

PDB ID:

6LLB 

Release:

2020-01-01

Title:

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Li, D.F., Hou, Y.J., Guo, L.

Citation:

Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.187R free:0.224

Equivalence Class: 

NR_all_81754.1 

Eq. Class Rep:

6LLB

NDB ID:

 6SVS

PDB ID:

6SVS 

Release:

2020-01-01

Title:

Crystal Structure of U:A-U-rich RNA triple helix with 11 consecutive base triples

Classification:

RNA

Authors:

Ruszkowska, A., Ruszkowski, M., Hulewicz, J.P., Dauter, Z., Brown, J.A.

Citation:

Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples.
Nucleic Acids Res. pp. - 2020

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.166R free:0.213

Equivalence Class: 

NR_all_70863.1 

Eq. Class Rep:

6SVS

NDB ID:

 6UGG

PDB ID:

6UGG 

Release:

2020-01-01

Title:

Structure of unmodified E. coli tRNA(Asp)

Classification:

RNA

Authors:

Chan, C.W., Badong, D., Rajan, R., Mondragon, A.

Citation:

Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.
Rna 26 pp.278 - 289 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.95Å R work:0.215R free:0.238

Equivalence Class: 

NR_all_56204.1 

Eq. Class Rep:

6UGG

NDB ID:

 6UGI

PDB ID:

6UGI 

Release:

2020-01-01

Title:

Crystal structure of a fragment of E. coli tRNA(Asp) consisting of its acceptor stem/T stem-loop. Long unit cell.

Classification:

RNA

Authors:

Chan, C.W., Badong, D., Rajan, R., Mondragon, A.

Citation:

Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.
Rna 26 pp.278 - 289 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.75Å R work:0.23R free:0.255

Equivalence Class: 

NR_all_92029.1 

Eq. Class Rep:

6UGI

NDB ID:

 6UGJ

PDB ID:

6UGJ 

Release:

2020-01-01

Title:

Crystal structure of a fragment of E. coli tRNA(Asp) consisting of its acceptor stem/T stem-loop. Short unit cell.

Classification:

RNA

Authors:

Chan, C.W., Badong, D., Rajan, R., Mondragon, A.

Citation:

Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs.
Rna 26 pp.278 - 289 2020

Experiment:

 X-RAY DIFFRACTION Resolution:1.6Å R work:0.213R free:0.272

Equivalence Class: 

NR_all_92029.1 

Eq. Class Rep:

6UGI

NDB ID:

 6UV1

PDB ID:

6UV1 

Release:

2020-01-01

Title:

Crystal structure of RNA helicase DDX17 in complex of rU10 RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Ngo, T.D., Partin, A.C., Nam, Y.

Citation:

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.
Cell Rep 29 pp.4024 - 4035.e5 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.307Å R work:0.197R free:0.255

Equivalence Class: 

NR_all_20040.1 

Eq. Class Rep:

6UV1

NDB ID:

 6UV1

PDB ID:

6UV1 

Release:

2020-01-01

Title:

Crystal structure of RNA helicase DDX17 in complex of rU10 RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Ngo, T.D., Partin, A.C., Nam, Y.

Citation:

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.
Cell Rep 29 pp.4024 - 4035.e5 2019

Experiment:

 X-RAY DIFFRACTION Resolution:2.307Å R work:0.197R free:0.255

Equivalence Class: 

NR_all_43929.1 

Eq. Class Rep:

6UV1

NDB ID:

 6UV2

PDB ID:

6UV2 

Release:

2020-01-01

Title:

Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo1

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Ngo, T.D., Partin, A.C., Nam, Y.

Citation:

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.
Cell Rep 29 pp.4024 - 4035.e5 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.894Å R work:0.169R free:0.19

Equivalence Class: 

NR_all_16093.1 

Eq. Class Rep:

6UV2

NDB ID:

 6UV3

PDB ID:

6UV3 

Release:

2020-01-01

Title:

Crystal structure of the core domain of RNA helicase DDX17 with RNA pri-125a-oligo2

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Ngo, T.D., Partin, A.C., Nam, Y.

Citation:

RNA Specificity and Autoregulation of DDX17, a Modulator of MicroRNA Biogenesis.
Cell Rep 29 pp.4024 - 4035.e5 2019

Experiment:

 X-RAY DIFFRACTION Resolution:1.597Å R work:0.174R free:0.197

Equivalence Class: 

NR_all_82332.1 

Eq. Class Rep:

6UV3

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