A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 17-Dec-2014 number of released structures: 7198
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 2604   (Gallery view)

NDB ID:

NA2821

PDB ID:

4NXH 

Release:

2014-12-10

Title:

2'-Trifluoromethylthiouridine-modified E. coli 23S rRNA Sarcin Ricin Loop

Classification:

RNA

Authors:

Ennifar, E., Micura, R., Kosutic, M.

Citation:

2'-Trifluoromethylthio-modified RNA: synthesis, X-ray structure, thermodynamic analysis, and applications
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.158Å R work:0.115R free:0.148

NDB ID:

NA3207

PDB ID:

4RGE 

Release:

2014-12-03

Title:

Crystal structure of the in-line aligned env22 twister ribozyme

Classification:

RNA

Authors:

Ren, A., Kosutic, M., Rajashankar, K.R., Frener, M., Santner, T., Westhof, E., Micura, R., Patel, D.J.

Citation:

In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.
Nat Commun 5 pp.5534 - 5534 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.89Å R work:0.177R free:0.222

Equivalence Class: 

NR_all_60141.1 

Eq. Class Rep:

4RGE

NDB ID:

NA3208

PDB ID:

4RGF 

Release:

2014-12-03

Title:

Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+

Classification:

RNA

Authors:

Ren, A., Kosutic, M., Rajashankar, K.R., Frener, M., Santner, T., Westhof, E., Micura, R., Patel, D.J.

Citation:

In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.
Nat Commun 5 pp.5534 - 5534 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2008Å R work:0.231R free:0.276

Equivalence Class: 

NR_all_60141.1 

Eq. Class Rep:

4RGE

NDB ID:

2MTV

PDB ID:

2MTV 

Release:

2014-11-26

Title:

Solution Structure of the YTH Domain of YT521-B in complex with N6-Methyladenosine containing RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Theler, D., Dominguez, C., Blatter, M., Boudet, J., Allain, F.H.

Citation:

Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.
Nucleic Acids Res. pp. - 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_21745.1 

Eq. Class Rep:

2MTV

NDB ID:

NA2987

PDB ID:

4Q5V 

Release:

2014-11-26

Title:

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and aphidicolin

Classification:

TRANSFERASE/DNA/RNA

Authors:

Baranovskiy, A.G., Babayeva, N.D., Suwa, Y., Gu, J., Pavlov, Y.I., Tahirov, T.H.

Citation:

Structural basis for inhibition of DNA replication by aphidicolin.
Nucleic Acids Res. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.52Å R work:0.232R free:0.268

Equivalence Class: 

NR_all_91301.4 

Eq. Class Rep:

1RRR

NDB ID:

NA2994

PDB ID:

4QCL 

Release:

2014-11-26

Title:

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP

Classification:

TRANSFERASE/DNA/RNA

Authors:

Baranovskiy, A.G., Babayeva, N.D., Suwa, Y., Gu, J., Tahirov, T.H.

Citation:

Crystal structure of human dna polymerase alpha catalytic core in complex with DNA/RNA and DCP
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.209R free:0.238

NDB ID:

NA2781

PDB ID:

4NLF 

Release:

2014-11-19

Title:

2'-trifluoromethylthio-2'-deoxycytidine-modified SRL

Classification:

RNA

Authors:

Ennifar, E., Micura, R., Kosutic, M.

Citation:

2'-Trifluoromethylthio-modified RNA: synthesis, X-ray structure, thermodynamic analysis, and applications
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.0Å R work:0.098R free:0.116

Equivalence Class: 

NR_all_09214.3 

Eq. Class Rep:

4NLF

NDB ID:

NA2782

PDB ID:

4NMG 

Release:

2014-11-19

Title:

2'-Trifluoromethylthio-2'-deoxyuridine-modified SRL

Classification:

RNA

Authors:

Ennifar, E., Micura, R., Kosutic, M.

Citation:

2'-Trifluoromethylthio-modified RNA: synthesis, X-ray structure, thermodynamic analysis, and applications
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.01Å R work:0.119R free:0.141

Equivalence Class: 

NR_all_09214.3 

Eq. Class Rep:

4NLF

NDB ID:

NA3254

PDB ID:

4RKV 

Release:

2014-11-19

Title:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions

Classification:

RNA

Authors:

Fyfe, A.C., Dunten, P.W., Scott, W.G.

Citation:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:0.88Å R work:0.092R free:0.098

Equivalence Class: 

NR_all_34192.1 

Eq. Class Rep:

4RKV

NDB ID:

NA3262

PDB ID:

4RNE 

Release:

2014-11-19

Title:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions

Classification:

RNA

Authors:

Fyfe, A.C., Dunten, P.W., Scott, W.G.

Citation:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.01Å R work:0.101R free:0.119

Equivalence Class: 

NR_all_34192.1 

Eq. Class Rep:

4RKV

NDB ID:

NA3295

PDB ID:

4RCM 

Release:

2014-11-19

Title:

Crystal structure of the Pho92 YTH domain in complex with m6A

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Tempel, W., Xu, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Citation:

Crystal structure of the Pho92 YTH domain in complex with m6A
TO BE PUBLISHED pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.217R free:0.268

NDB ID:

NA3300

PDB ID:

4CS1 

Release:

2014-11-19

Title:

Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound.

Classification:

RNA

Authors:

Mcphee, S.A., Huang, L., Lilley, D.M.J.

Citation:

A Critical Base Pair in K-Turns that Confers Folding Characteristics and Correlates with Biological Function.
Nat.Commun. 5 pp.5127 - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.184R free:0.234

Equivalence Class: 

NR_all_62099.1 

Eq. Class Rep:

4CS1

NDB ID:

NA2701

PDB ID:

4MCF 

Release:

2014-11-12

Title:

Crystal structure of the Gas5 GRE Mimic

Classification:

RNA

Authors:

Hudson, W.H., Pickard, M.R., de Vera, I.M., Kuiper, E.G., Mourtada-Maarabouni, M., Conn, G.L., Kojetin, D.J., Williams, G.T., Ortlund, E.A.

Citation:

Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate.
Nat Commun 5 pp.5395 - 5395 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.899Å R work:0.23R free:0.263

Equivalence Class: 

NR_all_25901.1 

Eq. Class Rep:

4MCF

NDB ID:

NA3171

PDB ID:

4RCJ 

Release:

2014-11-12

Title:

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Tempel, W., Xu, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Citation:

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA
TO BE PUBLISHED pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.6Å R work:0.171R free:0.209

Equivalence Class: 

NR_all_09340.1 

Eq. Class Rep:

4RCJ

NDB ID:

NA3218

PDB ID:

4RJ1 

Release:

2014-11-12

Title:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions

Classification:

RNA

Authors:

Fyfe, A.C., Dunten, P.W., Scott, W.G.

Citation:

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions.
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:0.92Å R work:0.091R free:0.108

Equivalence Class: 

NR_all_34192.1 

Eq. Class Rep:

4RKV

NDB ID:

4WF1

PDB ID:

4WF1 

Release:

2014-11-05

Title:

Crystal structure of the E. coli ribosome bound to negamycin.

Classification:

Ribosome/Antibiotic

Authors:

Olivier, N.B., Altman, R.B., Noeske, J., Basarab, G.S., Code, E., Ferguson, A.D., Gao, N., Huang, J., Juette, M.F., Livchak, S., Miller, M.D., Prince, D.B., Cate, J.H., Buurman, E.T., Blanchard, S.C.

Citation:

Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.
Proc.Natl.Acad.Sci.USA pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.09Å R work:0.201R free:0.244

NDB ID:

NA2943

PDB ID:

3WRU 

Release:

2014-11-05

Title:

Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA group

Classification:

RNA/antibiotic

Authors:

Maianti, J.P., Kanazawa, H., Dozzo, P., Matias, R.D., Feeney, L.A., Armstrong, E.S., Hildebrandt, D.J., Kane, T.R., Gliedt, M.J., Goldblum, A.A., Linsell, M.S., Aggen, J.B., Kondo, J., Hanessian, S.

Citation:

Toxicity Modulation, Resistance Enzyme Evasion, and A-Site X-ray Structure of Broad-Spectrum Antibacterial Neomycin Analogs
Acs Chem.Biol. 9 pp.2067 - 2073 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.248R free:0.261

Equivalence Class: 

NR_all_17243.9 

Eq. Class Rep:

1MWL

NDB ID:

NA3275

PDB ID:

4UYJ 

Release:

2014-11-05

Title:

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation

Classification:

SIGNALING PROTEIN

Authors:

Bousset, L., Mary, C., Brooks, M.A., Scherrer, A., Strub, K., Cusack, S.

Citation:

Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.
RNA 20 pp.1955 - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.35Å R work:0.192R free:0.236

Equivalence Class: 

NR_all_08631.1 

Eq. Class Rep:

4UYJ

NDB ID:

NA3276

PDB ID:

4UYK 

Release:

2014-11-05

Title:

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation

Classification:

SIGNALING PROTEIN

Authors:

Bousset, L., Mary, C., Brooks, M.A., Scherrer, A., Strub, K., Cusack, S.

Citation:

Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.
RNA 20 pp.1955 - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.22Å R work:0.191R free:0.233

Equivalence Class: 

NR_all_76150.1 

Eq. Class Rep:

4UYK

NDB ID:

NA2947

PDB ID:

4PR6 

Release:

2014-10-29

Title:

A Second Look at the HDV Ribozyme Structure and Dynamics.

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.

Citation:

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Nucleic Acids Res. 42 pp.12833 - 12846 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.198R free:0.24

Equivalence Class: 

NR_all_75503.2 

Eq. Class Rep:

1VBY

NDB ID:

NA2948

PDB ID:

4PRF 

Release:

2014-10-29

Title:

A Second Look at the HDV Ribozyme Structure and Dynamics.

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.

Citation:

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
Nucleic Acids Res. 42 pp.12833 - 12846 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.395Å R work:0.197R free:0.251

Equivalence Class: 

NR_all_75503.2 

Eq. Class Rep:

1VBY

NDB ID:

2MTJ

PDB ID:

2MTJ 

Release:

2014-10-22

Title:

NMR structure of the III-IV-V three-way junction from the VS ribozyme

Classification:

RNA

Authors:

Bonneau, E., Legault, P.

Citation:

Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.
Biochemistry 53 pp.6264 - 6275 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_52058.1 

Eq. Class Rep:

2MTJ

NDB ID:

2MTK

PDB ID:

2MTK 

Release:

2014-10-22

Title:

NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

Classification:

RNA

Authors:

Bonneau, E., Legault, P.

Citation:

Nuclear Magnetic Resonance Structure of the III-IV-V Three-Way Junction from the Varkud Satellite Ribozyme and Identification of Magnesium-Binding Sites Using Paramagnetic Relaxation Enhancement.
Biochemistry 53 pp.6264 - 6275 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_52058.1 

Eq. Class Rep:

2MTJ

NDB ID:

4U3M

PDB ID:

4U3M 

Release:

2014-10-22

Title:

Crystal structure of Anisomycin bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.198R free:0.245

NDB ID:

4U3N

PDB ID:

4U3N 

Release:

2014-10-22

Title:

Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.181R free:0.236

NDB ID:

4U3U

PDB ID:

4U3U 

Release:

2014-10-22

Title:

Crystal structure of Cycloheximide bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.204R free:0.244

NDB ID:

4U4N

PDB ID:

4U4N 

Release:

2014-10-22

Title:

Crystal structure of Edeine bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.203R free:0.251

NDB ID:

4U4O

PDB ID:

4U4O 

Release:

2014-10-22

Title:

Crystal structure of Geneticin bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.189R free:0.266

NDB ID:

4U4Q

PDB ID:

4U4Q 

Release:

2014-10-22

Title:

Crystal structure of Homoharringtonine bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.207R free:0.254

NDB ID:

4U4R

PDB ID:

4U4R 

Release:

2014-10-22

Title:

Crystal structure of Lactimidomycin bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.801Å R work:0.208R free:0.245

NDB ID:

4U4U

PDB ID:

4U4U 

Release:

2014-10-22

Title:

Crystal structure of Lycorine bound to the yeast 80S ribosome

Classification:

RIBOSOME

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.211R free:0.258

NDB ID:

4U4Y

PDB ID:

4U4Y 

Release:

2014-10-22

Title:

Crystal structure of Pactamycin bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.192R free:0.245

NDB ID:

4U4Z

PDB ID:

4U4Z 

Release:

2014-10-22

Title:

Crystal structure of Phyllanthoside bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.201R free:0.252

NDB ID:

4U50

PDB ID:

4U50 

Release:

2014-10-22

Title:

Crystal structure of Verrucarin bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.212R free:0.261

NDB ID:

4U51

PDB ID:

4U51 

Release:

2014-10-22

Title:

Crystal structure of Narciclasine bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.204R free:0.252

NDB ID:

4U52

PDB ID:

4U52 

Release:

2014-10-22

Title:

Crystal structure of Nagilactone C bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.206R free:0.257

NDB ID:

4U53

PDB ID:

4U53 

Release:

2014-10-22

Title:

Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.201R free:0.255

NDB ID:

4U55

PDB ID:

4U55 

Release:

2014-10-22

Title:

Crystal structure of Cryptopleurine bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.193R free:0.246

NDB ID:

4U56

PDB ID:

4U56 

Release:

2014-10-22

Title:

Crystal structure of Blasticidin S bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.45Å R work:0.195R free:0.259

NDB ID:

4U6F

PDB ID:

4U6F 

Release:

2014-10-22

Title:

Crystal structure of T-2 toxin bound to the yeast 80S ribosome

Classification:

ribosome

Authors:

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

Citation:

Structural basis for the inhibition of the eukaryotic ribosome.
Nature 513 pp.517 - 522 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.197R free:0.246

NDB ID:

2MFD

PDB ID:

2MFD 

Release:

2014-10-15

Title:

The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir404/03

Classification:

RNA

Authors:

Ihle, Y., Zell, R., Gorlach, M.

Citation:

The Solution Structure of a cGCUUAg RNA Pentaloop from Bovine Enterovirus Vir 404/03
To be Published pp. - 0

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_56845.1 

Eq. Class Rep:

2MFD

NDB ID:

4W2F

PDB ID:

4W2F 

Release:

2014-10-15

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Polikanov, Y.S., Osterman, I.A., Szal, T., Tashlitsky, V.N., Serebryakova, M.V., Kusochek, P., Bulkley, D., Malanicheva, I.A., Efimenko, T.A., Efremenkova, O.V., Konevega, A.L., Shaw, K.J., Bogdanov, A.A., Rodnina, M.V., Dontsova, O.A., Mankin, A.S., Steitz, T.A., Sergiev, P.V.

Citation:

Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome
To Be Published pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.237R free:0.277

NDB ID:

4W2G

PDB ID:

4W2G 

Release:

2014-10-15

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with pactamycin (soaked), mRNA and three deacylated tRNAs in the A, P and E sites

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Polikanov, Y.S., Osterman, I.A., Szal, T., Tashlitsky, V.N., Serebryakova, M.V., Kusochek, P., Bulkley, D., Malanicheva, I.A., Efimenko, T.A., Efremenkova, O.V., Konevega, A.L., Shaw, K.J., Bogdanov, A.A., Rodnina, M.V., Dontsova, O.A., Mankin, A.S., Steitz, T.A., Sergiev, P.V.

Citation:

Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome
To Be Published pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.225R free:0.273

NDB ID:

4W2H

PDB ID:

4W2H 

Release:

2014-10-15

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with pactamycin (co-crystallized), mRNA and deacylated tRNA in the P site

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Polikanov, Y.S., Osterman, I.A., Szal, T., Tashlitsky, V.N., Serebryakova, M.V., Kusochek, P., Bulkley, D., Malanicheva, I.A., Efimenko, T.A., Efremenkova, O.V., Konevega, A.L., Shaw, K.J., Bogdanov, A.A., Rodnina, M.V., Dontsova, O.A., Mankin, A.S., Steitz, T.A., Sergiev, P.V.

Citation:

Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome
To Be Published pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.215R free:0.262

NDB ID:

4W2I

PDB ID:

4W2I 

Release:

2014-10-15

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

Classification:

RIBOSOME/ANTIBIOTIC

Authors:

Polikanov, Y.S., Szal, T., Jiang, F., Gupta, P., Matsuda, R., Shiozuka, M., Steitz, T.A., Vazquez-Laslop, Nora, Mankin, A.S.

Citation:

Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA
To Be Published pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.209R free:0.256

NDB ID:

NA3057

PDB ID:

4QM6 

Release:

2014-10-08

Title:

Structure of bacterial polynucleotide kinase bound to GTP and RNA

Classification:

TRANSFERASE/RNA

Authors:

Das, U., Wang, L.K., Smith, P., Munir, A., Shuman, S.

Citation:

Structures of bacterial polynucleotide kinase in a Michaelis complex with NTPMg2+ and 5'-OH RNA and a mixed substrate-product complex with NTPMg2+ and a 5'-phosphorylated oligonucleotide.
J.Bacteriol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.5Å R work:0.153R free:0.174

Equivalence Class: 

NR_all_18022.1 

Eq. Class Rep:

4QM6

NDB ID:

2MNC

PDB ID:

2MNC 

Release:

2014-10-01

Title:

oligonucleotide model of miR-21 pre-element

Classification:

RNA

Authors:

Chirayil, S., Wu, Q., Amezcua, C., Luebke, K.J.

Citation:

NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element.
Plos One 9 pp.e108231 - e108231 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_26675.1 

Eq. Class Rep:

2MNC

NDB ID:

4P6F

PDB ID:

4P6F 

Release:

2014-10-01

Title:

Crystal structure of the peptolide 12C bound to bacterial ribosome

Classification:

Ribosome/Ribosome inhibitor

Authors:

Washington, A.Z., Benicewicz, D.B., Canzoneri, J.C., Fagan, C.E., Mwakwari, S.C., Maehigashi, T., Dunham, C.M., Oyelere, A.K.

Citation:

Macrolide-Peptide Conjugates as Probes of the Path of Travel of the Nascent Peptides through the Ribosome.
Acs Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.222R free:0.254

NDB ID:

4W29

PDB ID:

4W29 

Release:

2014-10-01

Title:

70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state.

Classification:

RIBOSOME/Antibiotic

Authors:

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

Citation:

How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation.
Science 345 pp.1188 - 1191 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.8Å R work:0.294R free:0.33

NDB ID:

4W2E

PDB ID:

4W2E 

Release:

2014-10-01

Title:

Crystal structure of Elongation Factor 4 (EF4/LepA) bound to the Thermus thermophilus 70S ribosome

Classification:

ribosome

Authors:

Gagnon, M.G., Lin, J., Bulkley, D., Steitz, T.A.

Citation:

Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome.
Science 345 pp.684 - 687 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.238R free:0.303