A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 11-Jan-2017 number of released structures: 8684
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 3210  Download results as an excel file       Gallery view

NDB ID:

5KPY

PDB ID:

5KPY 

Release:

2017-01-11

Title:

Structure of a 5-hydroxytryptophan aptamer

Classification:

RNA

Authors:

Porter, E.B., Polaski, J.T., Morck, M.M., Batey, R.T.

Citation:

Recurrent RNA motifs as scaffolds for genetically encodable small molecule biosensors
Nat.Chem.Biol. pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.216R free:0.258

NDB ID:

5MFX

PDB ID:

5MFX 

Release:

2017-01-11

Title:

Zika NS3 helicase:RNA complex

Classification:

HYDROLASE

Authors:

Jenkins, H.T., Ge, M., Chechik, M., Greive, S.J., Antson, A.A.

Citation:

How Zika virus NS3 helicase grips the first nucleotide of the leading RNA strand
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.598Å R work:0.161R free:0.191

NDB ID:

5MJV

PDB ID:

5MJV 

Release:

2017-01-11

Title:

Rebuild and re-refined model for Human Parechovirus 1

Classification:

VIRUS

Authors:

Shakeel, S., Dykeman, E.C., White, S.J., Ora, A., Cockburn, J.J.B., Butcher, S.J., Stockley, P.G., Twarock, R.

Citation:

Genomic RNA folding mediates assembly of human parechovirus
to be published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.09Å R work:0.258R free:0.261

NDB ID:

5T83

PDB ID:

5T83 

Release:

2017-01-11

Title:

Structure of a guanidine-I riboswitch from S. acidophilus

Classification:

RNA

Authors:

Reiss, C.W., Xiong, Y., Strobel, S.A.

Citation:

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.
Structure 25 pp.195 - 202 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.71Å R work:0.2R free:0.225

NDB ID:

5TDJ

PDB ID:

5TDJ 

Release:

2017-01-11

Title:

RNA decamer duplex with four 2'-5'-linkages

Classification:

RNA

Authors:

Shen, F., Luo, Z., Liu, H., Wang, R., Zhang, S., Gan, J., Sheng, J.

Citation:

Structural insights into RNA duplexes with multiple 2'-5'-linkages.
Nucleic Acids Res. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.152R free:0.17

NDB ID:

5TDK

PDB ID:

5TDK 

Release:

2017-01-11

Title:

RNA decamer duplex with eight 2'-5'-linkages

Classification:

RNA

Authors:

Shen, F., Luo, Z., Liu, H., Wang, R., Zhang, S., Gan, J., Sheng, J.

Citation:

Structural insights into RNA duplexes with multiple 2'-5'-linkages.
Nucleic Acids Res. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.43Å R work:0.167R free:0.205

NDB ID:

5TF6

PDB ID:

5TF6 

Release:

2017-01-11

Title:

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Montemayor, E.J., Didychuk, A.L., Liao, H., Hu, P., Brow, D.A., Butcher, S.E.

Citation:

Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core
Acta Crystallogr.,Sect.D 73 pp. - 2017

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.185R free:0.231

NDB ID:

5HAB

PDB ID:

5HAB 

Release:

2017-01-04

Title:

Crystal structure of mpy-RNase J (mutant H84A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA

Classification:

HYDROLASE

Authors:

Zheng, X., Feng, N., Li, D.F., Li, J., Dong, X.Z.

Citation:

Molecular insights into catalysis and processive exonucleolytic mechanisms of prokaryotic RNase J revealing striking parallels with that of eukaryotic Xrn1
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.206R free:0.24

NDB ID:

5H3U

PDB ID:

5H3U 

Release:

2016-12-28

Title:

Sm RNA bound to GEMIN5-WD

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Tang, X., Bharath, S.R., Piao, S., Tan, V.Q., Bowler, M.W., Song, H.

Citation:

Structural basis for specific recognition of pre-snRNA by Gemin5
Cell Res. 26 pp.1353 - 1356 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.499Å R work:0.201R free:0.256

NDB ID:

5HL7

PDB ID:

5HL7 

Release:

2016-12-21

Title:

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with lefamulin

Classification:

RIBOSOME

Authors:

Eyal, Z., Matzov, D., Krupkin, M., Paukner, S., Riedl, R., Rozenberg, H., Zimmerman, E., Bashan, A., Yonath, A.

Citation:

A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.
Sci Rep 6 pp.39004 - 39004 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.55Å R work:0.186R free:0.226

NDB ID:

5L2L

PDB ID:

5L2L 

Release:

2016-12-21

Title:

Nab2 Zn fingers 5-7 bound to A11G RNA

Classification:

RNA BINDING PROTEIN

Authors:

Aibara, S., Gordon, J.M., Riesterer, A.S., McLaughlin, S.H., Stewart, M.

Citation:

Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae.
Nucleic Acids Res. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.55Å R work:0.13R free:0.151

NDB ID:

5M3H

PDB ID:

5M3H 

Release:

2016-12-21

Title:

Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

Classification:

TRANSFERASE

Authors:

Lukarska, M., Fournier, G., Pflug, A., Resa-Infante, P., Reich, S., Naffakh, N., Cusack, S.

Citation:

Structural basis of an essential interaction between influenza polymerase and Pol II CTD.
Nature pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.209R free:0.244

NDB ID:

5M3J

PDB ID:

5M3J 

Release:

2016-12-21

Title:

Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD

Classification:

VIRAL PROTEIN

Authors:

Lukarska, M., Fournier, G., Pflug, A., Resa-Infante, P., Reich, S., Naffakh, N., Cusack, S.

Citation:

Structural basis of an essential interaction between influenza polymerase and Pol II CTD.
Nature pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.5Å R work:0.238R free:0.268

NDB ID:

5DGF

PDB ID:

5DGF 

Release:

2016-12-14

Title:

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog

Classification:

Ribosome

Authors:

Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.

Citation:

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.25R free:0.309

NDB ID:

5DGV

PDB ID:

5DGV 

Release:

2016-12-14

Title:

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog

Classification:

Ribosome

Authors:

Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.

Citation:

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.237R free:0.284

NDB ID:

5F6C

PDB ID:

5F6C 

Release:

2016-12-14

Title:

The structure of E. coli RNase E catalytically inactive mutant with RNA bound

Classification:

HYDROLASE

Authors:

Bandyra, K.J., Luisi, B.F.

Citation:

The structure of E. coli RNase E catalytically inactive mutant with RNA bound
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.002Å R work:0.174R free:0.249

NDB ID:

5J01

PDB ID:

5J01 

Release:

2016-12-14

Title:

Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.

Classification:

RNA

Authors:

Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F.

Citation:

Crystal structures of a group II intron lariat primed for reverse splicing.
Science 354 pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.39Å R work:0.204R free:0.233

NDB ID:

5J02

PDB ID:

5J02 

Release:

2016-12-14

Title:

Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+, MG2+ and an inactive 5' exon.

Classification:

RNA

Authors:

Costa, M., Walbott, H., Monachello, D., Westhof, E., Michel, F.

Citation:

Crystal structures of a group II intron lariat primed for reverse splicing.
Science 354 pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.493Å R work:0.202R free:0.227

NDB ID:

5LWJ

PDB ID:

5LWJ 

Release:

2016-12-14

Title:

Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.

Classification:

RNA

Authors:

Wolter, A.C., Weickhmann, A.K., Nasiri, A.H., Hantke, K., Ohlenschlager, O., Wunderlich, C.H., Kreutz, C., Duchardt-Ferner, E., Wohnert, J.

Citation:

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.
Angew. Chem. Int. Ed. Engl. 56 pp.401 - 404 2017

Experiment:

SOLUTION NMR

NDB ID:

5T7B

PDB ID:

5T7B 

Release:

2016-12-14

Title:

Argonaute-2 - 5'-(E)-vinylphosphonate 2'-O-methyl-uridine modified mrTTR guide RNA complex

Classification:

HYDROLASE/RNA

Authors:

Elkayam, E., Joshua-Tor, L.

Citation:

Protein structure
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.529Å R work:0.193R free:0.238

NDB ID:

5TPY

PDB ID:

5TPY 

Release:

2016-12-14

Title:

Crystal structure of an exonuclease resistant RNA from Zika virus

Classification:

RNA

Authors:

Akiyama, B.M., Laurence, H.M., Massey, A.R., Costantino, D.A., Xie, X., Yang, Y., Shi, P.Y., Nix, J.C., Beckham, J.D., Kieft, J.S.

Citation:

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease.
Science 354 pp.1148 - 1152 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.805Å R work:0.19R free:0.217

NDB ID:

5DHB

PDB ID:

5DHB 

Release:

2016-12-07

Title:

Cooperativity and Downstream Binding in RNA Replication

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.187R free:0.192

NDB ID:

5DHC

PDB ID:

5DHC 

Release:

2016-12-07

Title:

Cooperativity and Downstream Binding in RNA Replication

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.55Å R work:0.17R free:0.195

NDB ID:

5HBW

PDB ID:

5HBW 

Release:

2016-12-07

Title:

RNA primer-template complex with 2-methylimidazole-activated monomer analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.216R free:0.254

NDB ID:

5HBX

PDB ID:

5HBX 

Release:

2016-12-07

Title:

RNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding sites

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.7Å R work:0.212R free:0.248

NDB ID:

5HBY

PDB ID:

5HBY 

Release:

2016-12-07

Title:

RNA primer-template complex with 2-methylimidazole-activated monomer analogue-3 binding sites

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.18Å R work:0.153R free:0.165

NDB ID:

5K77

PDB ID:

5K77 

Release:

2016-12-07

Title:

Dbr1 in complex with 7-mer branched RNA

Classification:

HYDROLASE/RNA

Authors:

Clark, N.E., Katolik, A., Roberts, K., Taylor, A.B., Holloway, S.P., Schuermann, J.P., Montemayor, E.J., Stevens, S.W., Fitzpatrick, P.F., Damha, M.J., Hart, P.J.

Citation:

The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures
Proc.Natl.Acad.Sci.USA pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.17Å R work:0.181R free:0.222

NDB ID:

5K78

PDB ID:

5K78 

Release:

2016-12-07

Title:

Dbr1 in complex with 16-mer branched RNA

Classification:

HYDROLASE/RNA

Authors:

Clark, N.E., Katolik, A., Roberts, K., Taylor, A.B., Holloway, S.P., Schuermann, J.P., Montemayor, E.J., Stevens, S.W., Fitzpatrick, P.F., Damha, M.J., Hart, P.J.

Citation:

The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures
Proc.Natl.Acad.Sci.USA pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.64Å R work:0.194R free:0.245

NDB ID:

5KRG

PDB ID:

5KRG 

Release:

2016-12-07

Title:

RNA 15mer duplex binding with PZG monomer

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.6Å R work:0.205R free:0.233

NDB ID:

5L00

PDB ID:

5L00 

Release:

2016-12-07

Title:

Self-complimentary RNA 15mer binding with GMP monomers

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Wang, J., Szostak, J.W.

Citation:

Unusual Base-Pairing Interactions in Monomer-Template Complexes
Acs Cent.Sci. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.25Å R work:0.208R free:0.238

NDB ID:

5M73

PDB ID:

5M73 

Release:

2016-12-07

Title:

Structure of the human SRP S domain with SRP72 RNA-binding domain

Classification:

RNA BINDING PROTEIN

Authors:

Becker, M.M., Lapouge, K., Segnitz, B., Wild, K., Sinning, I.

Citation:

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction.
Nucleic Acids Res. pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.237R free:0.28

NDB ID:

5M74

PDB ID:

5M74 

Release:

2016-11-30

Title:

Rebuild and re-refined model for Human Parechovirus 1

Classification:

VIRUS

Authors:

Shakeel, S., Dykeman, E.C., White, S.J., Ora, A., Cockburn, J.J.B., Butcher, S.J., Stockley, P.G., Twarock, R.

Citation:

Genomic RNA folding mediates assembly of human parechovirus
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:3.09Å R work:0.258R free:0.261

NDB ID:

5E54

PDB ID:

5E54 

Release:

2016-11-23

Title:

Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser

Classification:

RNA

Authors:

Stagno, J.R., Liu, Y., Bhandari, Y.R., Conrad, C.E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D.R., White, T.A., Coe, J.D., Wiedorn, M.O., Knoska, J., Oberthuer, D., Tuckey, R.A., Yu, P., Dyba, M., Tarasov, S.G., Weierstall, U., Grant, T.D., Schwieters, C.D., Zhang, J., Ferre-D'Amare, A.R., Fromme, P., Draper, D.E., Liang, M., Hunter, M.S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N.A., Chapman, H.N., Spence, J.C., Woodson, S.A., Wang, Y.X.

Citation:

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Nature pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.213R free:0.256

NDB ID:

5H1K

PDB ID:

5H1K 

Release:

2016-11-23

Title:

Crystal structure of WD40 repeat domains of Gemin5 in complex with 13-nt U4 snRNA fragment

Classification:

SPLICING/RNA

Authors:

Jin, W., Wang, Y., Liu, C.P., Yang, N., Jin, M., Cong, Y., Wang, M., Xu, R.M.

Citation:

Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5
Genes Dev. 30 pp.2391 - 2403 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.17R free:0.206

NDB ID:

5H1L

PDB ID:

5H1L 

Release:

2016-11-23

Title:

Crystal structure of WD40 repeat domains of Gemin5 in complex with 7-nt U4 snRNA fragment

Classification:

SPLICING/RNA

Authors:

Jin, W., Wang, Y., Liu, C.P., Yang, N., Jin, M., Cong, Y., Wang, M., Xu, R.M.

Citation:

Structural basis for snRNA recognition by the double-WD40 repeat domain of Gemin5
Genes Dev. 30 pp.2391 - 2403 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.194R free:0.24

NDB ID:

5LYB

PDB ID:

5LYB 

Release:

2016-11-23

Title:

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn

Classification:

Ribosome

Authors:

Melnikov, S., Mailliot, J., Rigger, L., Neuner, S., Shin, B.S., Yusupova, G., Dever, T.E., Micura, R., Yusupov, M.

Citation:

Molecular insights into protein synthesis with proline residues.
EMBO Rep. 17 pp.1776 - 1784 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.25Å R work:0.207R free:0.248

NDB ID:

5SWD

PDB ID:

5SWD 

Release:

2016-11-23

Title:

Structure of the adenine riboswitch aptamer domain in an intermediate-bound state

Classification:

RNA

Authors:

Stagno, J.R., Liu, Y., Bhandari, Y.R., Conrad, C.E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D.R., White, T.A., Coe, J.D., Wiedorn, M.O., Knoska, J., Oberthuer, D., Tuckey, R.A., Yu, P., Dyba, M., Tarasov, S.G., Weierstall, U., Grant, T.D., Schwieters, C.D., Zhang, J., Ferre-D'Amare, A.R., Fromme, P., Draper, D.E., Liang, M., Hunter, M.S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N.A., Chapman, H.N., Spence, J.C., Woodson, S.A., Wang, Y.X.

Citation:

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Nature pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.194R free:0.229

NDB ID:

5SWE

PDB ID:

5SWE 

Release:

2016-11-23

Title:

Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography

Classification:

RNA

Authors:

Stagno, J.R., Liu, Y., Bhandari, Y.R., Conrad, C.E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D.R., White, T.A., Coe, J.D., Wiedorn, M.O., Knoska, J., Oberthuer, D., Tuckey, R.A., Yu, P., Dyba, M., Tarasov, S.G., Weierstall, U., Grant, T.D., Schwieters, C.D., Zhang, J., Ferre-D'Amare, A.R., Fromme, P., Draper, D.E., Liang, M., Hunter, M.S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N.A., Chapman, H.N., Spence, J.C., Woodson, S.A., Wang, Y.X.

Citation:

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Nature pp. - 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.348R free:0.379

NDB ID:

5TGA

PDB ID:

5TGA 

Release:

2016-11-23

Title:

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro

Classification:

Ribosome

Authors:

Melnikov, S., Mailliot, J., Rigger, L., Neuner, S., Shin, B.S., Yusupova, G., Dever, T.E., Micura, R., Yusupov, M.

Citation:

Molecular insights into protein synthesis with proline residues.
EMBO Rep. 17 pp.1776 - 1784 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.211R free:0.264

NDB ID:

5JJI

PDB ID:

5JJI 

Release:

2016-11-16

Title:

Rho transcription termination factor bound to rU7 and 6 ADP-BeF3 molecules

Classification:

TRANSCRIPTION/RNA

Authors:

Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.

Citation:

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.
Proc. Natl. Acad. Sci. U.S.A. 113 pp.E7691 - E7700 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.601Å R work:0.218R free:0.246

NDB ID:

5JJK

PDB ID:

5JJK 

Release:

2016-11-16

Title:

Rho transcription termination factor bound to rA7 and 6 ADP-BeF3 molecules

Classification:

TRANSCRIPTION/RNA

Authors:

Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.

Citation:

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.
Proc. Natl. Acad. Sci. U.S.A. 113 pp.E7691 - E7700 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.15Å R work:0.233R free:0.264

NDB ID:

5JJL

PDB ID:

5JJL 

Release:

2016-11-16

Title:

Rho transcription termination factor bound to rU8 and 5 ADP-BeF3 molecules

Classification:

TRANSCRIPTION/RNA

Authors:

Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M.

Citation:

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.
Proc. Natl. Acad. Sci. U.S.A. 113 pp.E7691 - E7700 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.231R free:0.266

NDB ID:

5EN1

PDB ID:

5EN1 

Release:

2016-11-09

Title:

Crystal structure of hnRNPA2B1 in complex with RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Wu, B.X., Su, S.C., Ma, J.B.

Citation:

Crystal structure of HNRNPA2B1 RRM1-RRM2 with RNA complex
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.58Å R work:0.191R free:0.236

NDB ID:

5JVG

PDB ID:

5JVG 

Release:

2016-11-09

Title:

The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin

Classification:

RIBOSOME

Authors:

Krupkin, M., Wekselman, I., Matzov, D., Eyal, Z., Diskin Posner, Y., Rozenberg, H., Zimmerman, E., Bashan, A., Yonath, A.

Citation:

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
Proc.Natl.Acad.Sci.USA 113 pp.E6796 - E6805 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.428Å R work:0.211R free:0.252

NDB ID:

5JVH

PDB ID:

5JVH 

Release:

2016-11-09

Title:

The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin

Classification:

RIBOSOME

Authors:

Krupkin, M., Wekselman, I., Matzov, D., Eyal, Z., Diskin Posner, Y., Rozenberg, H., Zimmerman, E., Bashan, A., Yonath, A.

Citation:

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
Proc.Natl.Acad.Sci.USA 113 pp.E6796 - E6805 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.58Å R work:0.203R free:0.247

NDB ID:

5GMF

PDB ID:

5GMF 

Release:

2016-11-02

Title:

Crystal structure of monkey TLR7 in complex with guanosine and polyU

Classification:

IMMUNE SYSTEM/RNA

Authors:

Zhang, Z., Ohto, U., Shibata, T., Krayukhina, E., Taoka, M., Yamauchi, Y., Tanji, H., Isobe, T., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA
Immunity 45 pp.737 - 748 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.207R free:0.243

NDB ID:

5GMG

PDB ID:

5GMG 

Release:

2016-11-02

Title:

Crystal structure of monkey TLR7 in complex with loxoribine and polyU

Classification:

IMMUNE SYSTEM/RNA

Authors:

Zhang, Z., Ohto, U., Shibata, T., Krayukhina, E., Taoka, M., Yamauchi, Y., Tanji, H., Isobe, T., Uchiyama, S., Miyake, K., Shimizu, T.

Citation:

Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA
Immunity 45 pp.737 - 748 2016

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.215R free:0.258

NDB ID:

5IEM

PDB ID:

5IEM 

Release:

2016-11-02

Title:

NMR structure of the 5'-terminal hairpin of the 7SK snRNA

Classification:

TRANSCRIPTION

Authors:

Bourbigot, S., Dock-Bregeon, A.C., Eberling, P., Coutant, J., Kieffer, B., Lebars, I.

Citation:

Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA.
Rna 22 pp.1844 - 1858 2016

Experiment:

SOLUTION NMR

NDB ID:

5K36

PDB ID:

5K36 

Release:

2016-11-02

Title:

Structure of an eleven component nuclear RNA exosome complex bound to RNA

Classification:

Hydrolase/RNA

Authors:

Zinder, J.C., Wasmuth, E.V., Lima, C.D.

Citation:

Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3.
Mol.Cell 64 pp.734 - 745 2016

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.201R free:0.248

NDB ID:

5GXH

PDB ID:

5GXH 

Release:

2016-10-26

Title:

The structure of the Gemin5 WD40 domain with AAUUUUUG

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Xu, C., Ishikawa, H., Izumikawa, K., Li, L., He, H., Nobe, Y., Yamauchi, Y., Shahjee, H.M., Wu, X.-H., Yu, Y.-T., Isobe, T., Takahashi, N., Min, J.

Citation:

Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly
Genes Dev. 30 pp.2376 - 2390 2016

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.161R free:0.196