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As of 21-Jan-2015 number of released structures: 7315
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 2658   (Gallery view)

NDB ID:

4WT8

PDB ID:

4WT8 

Release:

2015-01-21

Title:

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Classification:

RIBOSOME

Authors:

Amunts, A., Fiedorczuk, K., Truong, T.T., Chandler, J., Peter Greenberg, E., Ramakrishnan, V.

Citation:

Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics.
J.Mol.Biol. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.204R free:0.241

NDB ID:

4WUS

PDB ID:

4WUS 

Release:

2015-01-21

Title:

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Classification:

RIBOSOME

Authors:

Amunts, A., Fiedorczuk, K., Truong, T.T., Chandler, J., Peter Greenberg, E., Ramakrishnan, V.

Citation:

Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics.
J.Mol.Biol. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.204R free:0.241

NDB ID:

4WWE

PDB ID:

4WWE 

Release:

2015-01-21

Title:

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Classification:

ribosome

Authors:

Amunts, A., Fiedorczuk, K., Truong, T.T., Chandler, J., Peter Greenberg, E., Ramakrishnan, V.

Citation:

Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics.
J.Mol.Biol. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.204R free:0.241

NDB ID:

4WWT

PDB ID:

4WWT 

Release:

2015-01-21

Title:

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Classification:

RIBOSOME

Authors:

Amunts, A., Fiedorczuk, K., Truong, T.T., Chandler, J., Peter Greenberg, E., Ramakrishnan, V.

Citation:

Bactobolin A binds to a site on the 70S ribosome distinct from previously seen antibiotics.
J.Mol.Biol. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.204R free:0.241

NDB ID:

4WZJ

PDB ID:

4WZJ 

Release:

2015-01-14

Title:

Spliceosomal U4 snRNP core domain

Classification:

SPLICING

Authors:

Leung, A.K., Nagai, K., Li, J.

Citation:

Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.
Nature 473 pp.536 - 539 2011

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.176R free:0.223

NDB ID:

4PDQ

PDB ID:

4PDQ 

Release:

2015-01-07

Title:

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog

Classification:

RNA/ANTIBIOTIC

Authors:

Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Matias, R.D., Serio, A., Kondo, J.

Citation:

Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs
Chem Sci 5 pp.4621 - 4632 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.194R free:0.236

NDB ID:

4PJO

PDB ID:

4PJO 

Release:

2014-12-31

Title:

Minimal U1 snRNP

Classification:

SPLICING

Authors:

Kondo, Y., Oubridge, C., van Roon, A.M., Nagai, K.

Citation:

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Elife 4 pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.206R free:0.254

NDB ID:

4PKD

PDB ID:

4PKD 

Release:

2014-12-31

Title:

U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2

Classification:

GENE REGULATION

Authors:

Kondo, Y., Oubridge, C., van Roon, A.M., Nagai, K.

Citation:

Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Elife 4 pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.196R free:0.257

NDB ID:

4TYW

PDB ID:

4TYW 

Release:

2014-12-31

Title:

DEAD-box helicase Mss116 bound to ssRNA and ADP-BeF

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Mallam, A.L., Sidote, D.J., Lambowitz, A.M.

Citation:

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
Elife 4 pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.197Å R work:0.216R free:0.253

NDB ID:

4TYY

PDB ID:

4TYY 

Release:

2014-12-31

Title:

DEAD-box helicase Mss116 bound to ssRNA and CDP-BeF

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Mallam, A.L., Sidote, D.J., Lambowitz, A.M.

Citation:

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
Elife 4 pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.74Å R work:0.223R free:0.266

NDB ID:

4TZ0

PDB ID:

4TZ0 

Release:

2014-12-31

Title:

DEAD-box helicase Mss116 bound to ssRNA and GDP-BeF

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Mallam, A.L., Sidote, D.J., Lambowitz, A.M.

Citation:

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase.
Elife 4 pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.35Å R work:0.23R free:0.259

NDB ID:

4WJ3

PDB ID:

4WJ3 

Release:

2014-12-31

Title:

Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa

Classification:

LIGASE/RNA

Authors:

Suzuki, T., Nakamura, A., Kato, K., Soll, D., Tanaka, I., Sheppard, K., Yao, M.

Citation:

Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.705Å R work:0.292R free:0.328

NDB ID:

4WJ4

PDB ID:

4WJ4 

Release:

2014-12-31

Title:

Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid

Classification:

LIGASE/RNA

Authors:

Suzuki, T., Nakamura, A., Kato, K., Soll, D., Tanaka, I., Sheppard, K., Yao, M.

Citation:

Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
Proc.Natl.Acad.Sci.USA pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.294Å R work:0.189R free:0.224

NDB ID:

4PMI

PDB ID:

4PMI 

Release:

2014-12-24

Title:

Crystal structure of Rev and Rev-response-element RNA complex

Classification:

RNA binding protein/RNA

Authors:

Jayaraman, B., Crosby, D.C., Homer, C., Ribeiro, I., Mavor, D., Frankel, A.D.

Citation:

RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex.
Elife 4 pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.192R free:0.21

NDB ID:

4WWW

PDB ID:

4WWW 

Release:

2014-12-24

Title:

Crystal structure of the E. coli ribosome bound to CEM-101

Classification:

Ribosome/antibiotic

Authors:

Llano-Sotelo, B., Dunkle, J., Klepacki, D., Zhang, W., Fernandes, P., Cate, J.H., Mankin, A.S.

Citation:

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
Antimicrob. Agents Chemother. 54 pp.4961 - 4970 2010

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.2R free:0.251

NDB ID:

4WAL

PDB ID:

4WAL 

Release:

2014-12-17

Title:

Crystal structure of selenomethionine Msl5 protein in complex with RNA at 2.2 A

Classification:

PROTEIN BINDING/RNA

Authors:

Jacewicz, A., Chico, L., Smith, P., Schwer, B., Shuman, S.

Citation:

Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs
Rna pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.2Å R work:0.172R free:0.215

NDB ID:

4WAN

PDB ID:

4WAN 

Release:

2014-12-17

Title:

Crystal structure of Msl5 protein in complex with RNA at 1.8 A

Classification:

PROTEIN BINDING/RNA

Authors:

Jacewicz, A., Chico, L., Smith, P., Schwer, B., Shuman, S.

Citation:

Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs
Rna pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.174R free:0.206

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. 42 pp.13911 - 13919 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. 42 pp.14013 - 14021 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:

4WRT

PDB ID:

4WRT 

Release:

2014-11-19

Title:

Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)

Classification:

TRANSFERASE/RNA

Authors:

Reich, S., Guilligay, D., Pflug, A., Malet, H., Berger, I., Crepin, T., Hart, D., Lunardi, T., Nanao, M., Ruigrok, R.W., Cusack, S.

Citation:

Structural insight into cap-snatching and RNA synthesis by influenza polymerase.
Nature 516 pp.361 - 366 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.7Å R work:0.173R free:0.211

Equivalence Class: 

NR_all_79304.1 

Eq. Class Rep:

4WRT

NDB ID:

4WSA

PDB ID:

4WSA 

Release:

2014-11-19

Title:

Crystal structure of Influenza B polymerase bound to the vRNA promoter (FluB1 form)

Classification:

TRANSFERASE/RNA

Authors:

Reich, S., Guilligay, D., Pflug, A., Malet, H., Berger, I., Crepin, T., Hart, D., Lunardi, T., Nanao, M., Ruigrok, R.W., Cusack, S.

Citation:

Structural insight into cap-snatching and RNA synthesis by influenza polymerase.
Nature 516 pp.361 - 366 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.4Å R work:0.228R free:0.265

Equivalence Class: 

NR_all_44542.1 

Eq. Class Rep:

4WSA

NDB ID:

4WSB

PDB ID:

4WSB 

Release:

2014-11-19

Title:

Bat Influenza A polymerase with bound vRNA promoter

Classification:

transferase/rna

Authors:

Reich, S., Guilligay, D., Pflug, A., Malet, H., Berger, I., Crepin, T., Hart, D., Lunardi, T., Nanao, M., Ruigrok, R.W., Cusack, S.

Citation:

Structural insight into cap-snatching and RNA synthesis by influenza polymerase.
Nature 516 pp.355 - 360 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.65Å R work:0.215R free:0.267

Equivalence Class: 

NR_all_71358.1 

Eq. Class Rep:

4WSB

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:

4W5N

PDB ID:

4W5N 

Release:

2014-11-12

Title:

The Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA

Classification:

HYDROLASE/RNA

Authors:

Schirle, N.T., Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Gene regulation. Structural basis for microRNA targeting.
Science 346 pp.608 - 613 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.217R free:0.253

Equivalence Class: 

NR_all_09481.1 

Eq. Class Rep:

4W5N

NDB ID:

4W5O

PDB ID:

4W5O 

Release:

2014-11-12

Title:

The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-9

Classification:

HYDROLASE/RNA

Authors:

Schirle, N.T., Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Gene regulation. Structural basis for microRNA targeting.
Science 346 pp.608 - 613 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.802Å R work:0.167R free:0.196

Equivalence Class: 

NR_all_67722.1 

Eq. Class Rep:

4W5O

NDB ID:

4W5Q

PDB ID:

4W5Q 

Release:

2014-11-12

Title:

The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-8

Classification:

HYDROLASE/RNA

Authors:

Schirle, N.T., Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Gene regulation. Structural basis for microRNA targeting.
Science 346 pp.608 - 613 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.101Å R work:0.19R free:0.232

Equivalence Class: 

NR_all_57000.1 

Eq. Class Rep:

4W5Q

NDB ID:

4W5R

PDB ID:

4W5R 

Release:

2014-11-12

Title:

The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-8 (Long Target)

Classification:

HYDROLASE/RNA

Authors:

Schirle, N.T., Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Gene regulation. Structural basis for microRNA targeting.
Science 346 pp.608 - 613 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.194R free:0.233

Equivalence Class: 

NR_all_99729.1 

Eq. Class Rep:

4W5R

NDB ID:

4W5T

PDB ID:

4W5T 

Release:

2014-11-12

Title:

The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-7

Classification:

HYDROLASE/RNA

Authors:

Schirle, N.T., Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Gene regulation. Structural basis for microRNA targeting.
Science 346 pp.608 - 613 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.172R free:0.215

Equivalence Class: 

NR_all_25317.1 

Eq. Class Rep:

4W5T

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 111 pp.16274 - 16279 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:

4PCJ

PDB ID:

4PCJ 

Release:

2014-10-29

Title:

Modifications to toxic CUG RNAs induce structural stability and rescue mis-splicing in Myotonic Dystrophy

Classification:

RNA

Authors:

deLorimier, E., Coonrod, L.A., Copperman, J., Taber, A., Reister, E.E., Sharma, K., Todd, P.K., Guenza, M.G., Berglund, J.A.

Citation:

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model.
Nucleic Acids Res. 42 pp.12768 - 12778 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.196R free:0.267

Equivalence Class: 

NR_all_14335.1 

Eq. Class Rep:

4PCJ

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