A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 15-May-2018 number of released structures: 9482
Search for released structures

RNA Search Options:

Polymer

All
RNA Only
Protein RNA Complexes
Drug RNA Complexes
Hybrids and Chimera
Peptide Nucleic Acid / Mimetics

RNA Type

All
tRNA
tRNA fragment
Ribosome
Ribozyme
Hairpin Ribozyme
Hammerhead Ribozyme
Group I intron Ribozyme
Group II intron Ribozyme
Rnase P Ribozyme
Polymerase Ribozyme
Ligase Ribozyme
Leadzyme
Ribozyme fragment
Virus
Viral fragment
Riboswitch
Riboswitch fragment
Aptamer
Telomerase RNA
Small nucleotide fragments
Double Helices
Triple Helices
Quadruple Helices

Protein Function

All
Enzymes
Structural
Regulatory

Experimental Method

All
XRAY
NMR

Representative RNA 3D Structure Sets

All RNA Structures
Representative sets of RNA-containing 3D structures
Resolution cutoff:

Text Search

Filter results by text search

Use this option to narrow your results down considerably (>50% reduction) using any word seen in the results page. Eg: Any author name found in the right side



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

Results: 4530  Download results as an excel file       Gallery view

NDB ID:

 5NPM

PDB ID:

5NPM 

Release:

2018-05-16

Title:

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

Classification:

RNA

Authors:

Gabdulkhakov, A.G., Tishchenko, T.V., Nevskaya, N.A., Nikonov, S.V., Garber, M.B.

Citation:

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.201R free:0.248

NDB ID:

 5VSU

PDB ID:

5VSU 

Release:

2018-05-09

Title:

Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA

Classification:

SPLICING

Authors:

Montemayor, E.J., Didychuk, A.L., Yake, A.D., Sidhu, G.K., Brow, D.A., Butcher, S.E.

Citation:

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Nat Commun 9 pp.1749 - 1749 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.233R free:0.298

NDB ID:

 6ASO

PDB ID:

6ASO 

Release:

2018-05-09

Title:

Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA

Classification:

SPLICING

Authors:

Montemayor, E.J., Didychuk, A.L., Yake, A.D., Sidhu, G.K., Brow, D.A., Butcher, S.E.

Citation:

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Nat Commun 9 pp.1749 - 1749 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.71Å R work:0.194R free:0.246

NDB ID:

 6FPQ

PDB ID:

6FPQ 

Release:

2018-05-09

Title:

Structure of S. pombe Mmi1 in complex with 7-mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Stowell, J.A.W., Wagstaff, J.L., Hill, C.H., Yu, M., McLaughlin, S.H., Freund, S.M.V., Passmore, L.A.

Citation:

A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.
J. Biol. Chem. pp. - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:1.42Å R work:0.142R free:0.167

NDB ID:

 6FPX

PDB ID:

6FPX 

Release:

2018-05-09

Title:

Structure of S. pombe Mmi1 in complex with 11-mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Stowell, J.A.W., Wagstaff, J.L., Hill, C.H., Yu, M., McLaughlin, S.H., Freund, S.M.V., Passmore, L.A.

Citation:

A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding.
J. Biol. Chem. pp. - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:1.97Å R work:0.2R free:0.234

NDB ID:

 6FQ3

PDB ID:

6FQ3 

Release:

2018-05-09

Title:

Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with lin-29A 5'UTR 13mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Kumari, P., Aeschimann, F., Gaidatzis, D., Keusch, J.J., Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H., Grosshans, H., Ciosk, R.

Citation:

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Nat Commun 9 pp.1549 - 1549 2018

Experiment:

 X-RAY DIFFRACTION Resolution:1.901Å R work:0.158R free:0.18

NDB ID:

 6FQL

PDB ID:

6FQL 

Release:

2018-05-09

Title:

Crystal structure of Danio rerio Lin41 filamin-NHL domains in complex with mab-10 3'UTR 13mer RNA

Classification:

RNA BINDING PROTEIN

Authors:

Kumari, P., Aeschimann, F., Gaidatzis, D., Keusch, J.J., Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H., Grosshans, H., Ciosk, R.

Citation:

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Nat Commun 9 pp.1549 - 1549 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.349Å R work:0.171R free:0.21

NDB ID:

 5NDJ

PDB ID:

5NDJ 

Release:

2018-05-02

Title:

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

Classification:

RIBOSOME

Authors:

Prokhorova, I., Altman, R.B., Djumagulov, M., Shrestha, J.P., Urzhumtsev, A., Ferguson, A., Chang, C.T., Yusupov, M., Blanchard, S.C., Yusupova, G.

Citation:

Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Proc. Natl. Acad. Sci. U.S.A. 114 pp.E10899 - E10908 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.15Å R work:0.202R free:0.246

NDB ID:

 5USB

PDB ID:

5USB 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (rGGTTACGGT)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

 X-RAY DIFFRACTION Resolution:1.615Å R work:0.175R free:0.202

NDB ID:

 5USN

PDB ID:

5USN 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (rGrGrUTACGGT)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

 X-RAY DIFFRACTION Resolution:1.9Å R work:0.183R free:0.223

NDB ID:

 5USO

PDB ID:

5USO 

Release:

2018-04-18

Title:

Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera (GGTTACrGrGrU)

Classification:

DNA BINDING PROTEIN/DNA/RNA

Authors:

Lloyd, N.R., Wuttke, D.S.

Citation:

Discrimination against RNA Backbones by a ssDNA Binding Protein.
Structure 26 pp.722 - 733.e2 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.0Å R work:0.21R free:0.245

NDB ID:

 5XPA

PDB ID:

5XPA 

Release:

2018-04-18

Title:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand

Classification:

DNA BINDING PROTEIN

Authors:

Sheng, G., Gogakos, T., Wang, J., Zhao, H., Serganov, A., Juranek, S., Tuschl, T., Patel, J.D., Wang, Y.

Citation:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.9Å R work:0.215R free:0.28

NDB ID:

 5XPG

PDB ID:

5XPG 

Release:

2018-04-18

Title:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on the target strand

Classification:

DNA BINDING PROTEIN

Authors:

Sheng, G., Gogakos, T., Wang, J., Zhao, H., Serganov, A., Juranek, S., Tuschl, T., Patel, J.D., Wang, Y.

Citation:

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 4A5 on the guide strand
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.202R free:0.246

NDB ID:

 6CAE

PDB ID:

6CAE 

Release:

2018-04-18

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution

Classification:

RIBOSOME/INHIBITOR

Authors:

Pantel, L., Florin, T., Dobosz-Bartoszek, M., Racine, E., Sarciaux, M., Serri, M., Houard, J., Campagne, J.M., de Figueiredo, R.M., Midrier, C., Gaudriault, S., Givaudan, A., Lanois, A., Forst, S., Aumelas, A., Cotteaux-Lautard, C., Bolla, J.M., Vingsbo Lundberg, C., Huseby, D.L., Hughes, D., Villain-Guillot, P., Mankin, A.S., Polikanov, Y.S., Gualtieri, M.

Citation:

Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site.
Mol. Cell 70 pp.83 - 94.e7 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.211R free:0.249

NDB ID:

 6CBD

PDB ID:

6CBD 

Release:

2018-04-18

Title:

Crystal Structure of Human Argonaute2 Bound to Three Tryptophans

Classification:

RNA BINDING PROTEIN

Authors:

Sheu-Gruttadauria, J., MacRae, I.J.

Citation:

Phase Transitions in the Assembly and Function of Human miRISC.
Cell 173 pp.946 - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.203Å R work:0.175R free:0.215

NDB ID:

 6C6K

PDB ID:

6C6K 

Release:

2018-04-04

Title:

Structural basis for preferential recognition of cap 0 RNA by a human IFIT1-IFIT3 protein complex

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Johnson, B., VanBlargan, L.A., Xu, W., White, J.P., Shan, C., Shi, P.Y., Zhang, R., Adhikari, J., Gross, M.L., Leung, D.W., Diamond, M.S., Amarasinghe, G.K.

Citation:

Human IFIT3 Modulates IFIT1 RNA Binding Specificity and Protein Stability.
Immunity 48 pp.487 - 499.e5 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.54Å R work:0.168R free:0.236

NDB ID:

 5V8I

PDB ID:

5V8I 

Release:

2018-03-28

Title:

Thermus thermophilus 70S ribosome lacking ribosomal protein uS17

Classification:

RIBOSOME

Authors:

Murphy, E., Connetti, J.L., Dahlberg, A.E., Gregory, S.T., Jogl, G.

Citation:

Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17
To be published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.25Å R work:0.226R free:0.27

NDB ID:

 6FKR

PDB ID:

6FKR 

Release:

2018-03-28

Title:

Crystal structure of the dolphin proline-rich antimicrobial peptide Tur1A bound to the Thermus thermophilus 70S ribosome

Classification:

RIBOSOME

Authors:

Mardirossian, M., Perebaskine, N., Benincasa, M., Gambato, S., Hofmann, S., Huter, P., Muller, C., Hilpert, K., Innis, C.A., Tossi, A., Wilson, D.N.

Citation:

The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome.
Cell Chem Biol pp. - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.2Å R work:0.189R free:0.251

NDB ID:

 5ZEG

PDB ID:

5ZEG 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.4Å R work:0.177R free:0.215

NDB ID:

 5ZEI

PDB ID:

5ZEI 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with geneticin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.2R free:0.25

NDB ID:

 5ZEJ

PDB ID:

5ZEJ 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex with paromomycin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.5Å R work:0.205R free:0.228

NDB ID:

 5ZEM

PDB ID:

5ZEM 

Release:

2018-03-21

Title:

Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in the presence of gentamicin

Classification:

RNA

Authors:

Kanazawa, H., Baba, F., Koganei, M., Kondo, J.

Citation:

A structural basis for the antibiotic resistance conferred by an N1-methylation of A1408 in 16S rRNA.
Nucleic Acids Res. 45 pp.12529 - 12535 2017

Experiment:

 X-RAY DIFFRACTION Resolution:3.103Å R work:0.255R free:0.283

NDB ID:

 5N5C

PDB ID:

5N5C 

Release:

2018-03-14

Title:

NMR solution structure of the TSL2 RNA hairpin

Classification:

RNA

Authors:

Garcia-Lopez, A., Wacker, A., Tessaro, F., Jonker, H.R.A., Richter, C., Comte, A., Berntenis, N., Schmucki, R., Hatje, K., Sciarra, D., Konieczny, P., Fournet, G., Faustino, I., Orozco, M., Artero, R., Goekjian, P., Metzger, F., Ebeling, M., Joseph, B., Schwalbe, H., Scapozza, L.

Citation:

Rational targeting of RNA structure in SMN2 transcripts reverses Spinal Muscular Atrophy molecular phenotypes
To be published pp. - 0

Experiment:

 SOLUTION NMR

NDB ID:

 5N94

PDB ID:

5N94 

Release:

2018-03-14

Title:

Crystal Structure of Drosophila DHX36 helicase in complex with polyU

Classification:

HYDROLASE

Authors:

Chen, W.F., Rety, S., Guo, H.L., Dai, Y.X., Wu, W.Q., Liu, N.N., Auguin, D., Liu, Q.W., Hou, X.M., Dou, S.X., Xi, X.G.

Citation:

Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.
Structure 26 pp.403 - 415.e4 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.428Å R work:0.211R free:0.277

NDB ID:

 5THE

PDB ID:

5THE 

Release:

2018-03-14

Title:

Crystal structure of the C-terminal lobe of a budding yeast Argonaute

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Dayeh, D.M., Kruithoff, B.C., Nakanishi, K.

Citation:

Structural and functional analyses reveal the contributions of the C- and N-lobes of Argonaute protein to selectivity of RNA target cleavage.
J. Biol. Chem. 293 pp.6308 - 6325 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.097Å R work:0.157R free:0.205

NDB ID:

 5YKI

PDB ID:

5YKI 

Release:

2018-03-14

Title:

Crystal structure of the engineered nine-repeat PUF domain in complex with cognate 9nt-RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Zhao, Y.Y., Mao, M.W., Zhang, W.J., Wang, J., Li, H.T., Yang, Y., Wang, Z., Wu, J.W.

Citation:

Expanding RNA binding specificity and affinity of engineered PUF domains.
Nucleic Acids Res. pp. - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.25Å R work:0.196R free:0.236

NDB ID:

 6CFJ

PDB ID:

6CFJ 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with histidyl-CAM and bound to mRNA and A-, P-, and E-site tRNAs at 2.8A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.214R free:0.268

NDB ID:

 6CFK

PDB ID:

6CFK 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with D-histidyl-CAM and bound to protein Y (YfiA) at 2.7A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.205R free:0.252

NDB ID:

 6CFL

PDB ID:

6CFL 

Release:

2018-03-07

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with lysyl-CAM and bound to protein Y (YfiA) at 2.6A resolution

Classification:

ribosome/inhibitor

Authors:

Tereshchenkov, A.G., Dobosz-Bartoszek, M., Osterman, I.A., Marks, J., Sergeeva, V.A., Kasatsky, P., Komarova, E.S., Stavrianidi, A.N., Rodin, I.A., Konevega, A.L., Sergiev, P.V., Sumbatyan, N.V., Mankin, A.S., Bogdanov, A.A., Polikanov, Y.S.

Citation:

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.
J. Mol. Biol. 430 pp.842 - 852 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.208R free:0.251

NDB ID:

 5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_03510.19 

Eq. Class Rep:

4V88

NDB ID:

 5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_18586.20 

Eq. Class Rep:

5TBW

NDB ID:

 5ON6

PDB ID:

5ON6 

Release:

2018-02-28

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Classification:

RIBOSOME

Authors:

Pellegrino, S., Meyer, M., Zorbas, C., Bouchta, S.A., Saraf, K., Pelly, S.C., Yusupova, G., Evidente, A., Mathieu, V., Kornienko, A., Lafontaine, D.L.J., Yusupov, M.

Citation:

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure 26 pp.416 - 425.e4 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.1Å R work:0.221R free:0.252

Equivalence Class: 

NR_all_90506.20 

Eq. Class Rep:

5TBW

NDB ID:

 5UZA

PDB ID:

5UZA 

Release:

2018-02-28

Title:

Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)

Classification:

RNA

Authors:

Liu, Y., Holmstrom, E., Yu, P., Tan, K., Zuo, X., Nesbitt, D.J., Sousa, R., Stagno, J.R., Wang, Y.X.

Citation:

Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.
Nat Protoc 13 pp.987 - 1005 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.22Å R work:0.215R free:0.25

Equivalence Class: 

NR_all_59689.4 

Eq. Class Rep:

4XNR

NDB ID:

 5X70

PDB ID:

5X70 

Release:

2018-02-28

Title:

Crystal structure of Rice Dwarf Virus P5 in complex with a ssRNA oligomer

Classification:

TRANSFERASE/RNA

Authors:

Nakamichi, Y., Higashiura, A., Narita, H., Hagiwara, K., Uehara-Ichiki, T., Omura, T., Nakagawa, A.

Citation:

Crystal structure of capping enzyme from Rice dwarf virus
To Be Published pp. - 0

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.22R free:0.268

Equivalence Class: 

NR_all_10013.1 

Eq. Class Rep:

5X70

NDB ID:

 6BJY

PDB ID:

6BJY 

Release:

2018-02-28

Title:

VSV Nucleocapsid with Polyamide Bound

Classification:

rna binding protein/rna

Authors:

Gumpper, R.H., Li, W., Castaneda, C.H., Scuderi, M.J., Bashkin, J.K., Luo, M.

Citation:

A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid.
J. Virol. 92 pp. - 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.46Å R work:0.265R free:0.31

Equivalence Class: 

NR_all_88517.3 

Eq. Class Rep:

4JNG

NDB ID:

 6BLO

PDB ID:

6BLO 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i+1 position

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.401Å R work:0.202R free:0.227

Equivalence Class: 

NR_all_45110.1 

Eq. Class Rep:

6BLO

NDB ID:

 6BLP

PDB ID:

6BLP 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i+1 position, soaking AMPCPP

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.203Å R work:0.214R free:0.256

Equivalence Class: 

NR_all_45110.1 

Eq. Class Rep:

6BLO

NDB ID:

 6BM2

PDB ID:

6BM2 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i-1 position

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.403Å R work:0.218R free:0.243

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

 6BM4

PDB ID:

6BM4 

Release:

2018-02-28

Title:

Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP

Classification:

TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.951Å R work:0.234R free:0.26

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

 6BQF

PDB ID:

6BQF 

Release:

2018-02-28

Title:

Pol II elongation complex with 'dT-AP' at i+1, i-1 position

Classification:

TRANSFERASE/TRANSCRIPTION

Authors:

Wang, W., Walmacq, C., Chong, J., Kashlev, M., Wang, D.

Citation:

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A. 115 pp.E2538 - E2545 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.35Å R work:0.217R free:0.244

Equivalence Class: 

NR_all_84294.1 

Eq. Class Rep:

6BM2

NDB ID:

 5N8L

PDB ID:

5N8L 

Release:

2018-02-21

Title:

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B)

Classification:

RNA BINDING PROTEIN

Authors:

Masliah, G., Maris, C., Konig, S.L., Yulikov, M., Aeschimann, F., Malinowska, A.L., Mabille, J., Weiler, J., Holla, A., Hunziker, J., Meisner-Kober, N., Schuler, B., Jeschke, G., Allain, F.H.

Citation:

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.
EMBO J. 37 pp. - 2018

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_25711.1 

Eq. Class Rep:

5N8L

NDB ID:

 5N8M

PDB ID:

5N8M 

Release:

2018-02-21

Title:

Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex A)

Classification:

RNA BINDING PROTEIN

Authors:

Masliah, G., Maris, C., Konig, S.L., Yulikov, M., Aeschimann, F., Malinowska, A.L., Mabille, J., Weiler, J., Holla, A., Hunziker, J., Meisner-Kober, N., Schuler, B., Jeschke, G., Allain, F.H.

Citation:

Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.
EMBO J. 37 pp. - 2018

Experiment:

 SOLUTION NMR

Equivalence Class: 

NR_all_25711.1 

Eq. Class Rep:

5N8L

NDB ID:

 5UX3

PDB ID:

5UX3 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.5Å R work:0.218R free:0.261

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

 5UZ6

PDB ID:

5UZ6 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImp-oligo analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.1Å R work:0.221R free:0.266

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

 5V0O

PDB ID:

5V0O 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG analogue bound

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.7Å R work:0.217R free:0.276

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

 5V9Z

PDB ID:

5V9Z 

Release:

2018-02-21

Title:

RNA hairpin structure containing 2-MeImpG analogue bound

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.51Å R work:0.218R free:0.281

Equivalence Class: 

NR_all_48359.1 

Eq. Class Rep:

5UZ6

NDB ID:

 5VCF

PDB ID:

5VCF 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.8Å R work:0.163R free:0.213

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

 5VCI

PDB ID:

5VCI 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif, complexed with 2-MeImpG analogue

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.6Å R work:0.162R free:0.212

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

 5VGW

PDB ID:

5VGW 

Release:

2018-02-21

Title:

RNA hairpin structure containing tetraloop/receptor motif

Classification:

RNA

Authors:

Zhang, W., Tam, C.P., Zhou, L., Oh, S.S., Wang, J., Szostak, J.W.

Citation:

Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
J. Am. Chem. Soc. 140 pp.2829 - 2840 2018

Experiment:

 X-RAY DIFFRACTION Resolution:2.42Å R work:0.207R free:0.212

Equivalence Class: 

NR_all_08052.1 

Eq. Class Rep:

5VCI

NDB ID:

 5WNP

PDB ID:

5WNP 

Release:

2018-02-21

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

RIBOSOME

Authors:

Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K.W., Wang, J., Petrov, A., Prabhakar, A., Rechavi, G., Dominissini, D., He, C., Ehrenberg, M., Puglisi, J.D.

Citation:

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.
Nat. Struct. Mol. Biol. 25 pp.208 - 216 2018

Experiment:

 X-RAY DIFFRACTION Resolution:3.3Å R work:0.191R free:0.224

Equivalence Class: 

NR_all_65795.29 

Eq. Class Rep:

4LFB

ndbadmin@ndbserver.rutgers.edu ©1995-2017 The Nucleic Acid Database Project | Rutgers, The State University of New Jersey