A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 29-Jul-2015 number of released structures: 7569
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
Other

Experimental Method

All
XRAY
NMR

Non-redundant List

All RNA Structures
Non Redundant RNA 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: 2778  Download results as an excel file       Gallery view

NDB ID:

4U3L

PDB ID:

4U3L 

Release:

2015-07-29

Title:

octameric RNA duplex co-crystallized in calcium(II)chloride

Classification:

RNA

Authors:

Schaffer, M.F., Spingler, B., Schnabl, J., Peng, G., Olieric, V., Sigel, R.K.O.

Citation:

The X-ray structures of an octameric RNA duplex in presence of six di- and trivalent metal ions
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.482Å R work:0.169R free:0.188

NDB ID:

4U3O

PDB ID:

4U3O 

Release:

2015-07-29

Title:

Octameric RNA duplex soaked in manganese(II)chloride

Classification:

RNA

Authors:

Schaffer, M.F., Spingler, B., Schnabl, J., Peng, G., Olieric, V., Sigel, R.K.O.

Citation:

The X-ray structures of an octameric RNA duplex in presence of six di- and trivalent metal ions
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.8Å R work:0.164R free:0.175

NDB ID:

4U3P

PDB ID:

4U3P 

Release:

2015-07-29

Title:

Octameric RNA duplex co-crystallized with strontium(II)chloride

Classification:

RNA

Authors:

Schaffer, M.F., Spingler, B., Schnabl, J., Peng, G., Olieric, V., Sigel, R.K.O.

Citation:

The X-ray structures of an octameric RNA duplex in presence of six di- and trivalent metal ions
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.866Å R work:0.179R free:0.229

NDB ID:

4U3R

PDB ID:

4U3R 

Release:

2015-07-29

Title:

Octameric RNA duplex co-crystallized with cobalt(II)chloride

Classification:

RNA

Authors:

Schaffer, M.F., Spingler, B., Schnabl, J., Peng, G., Olieric, V., Sigel, R.K.O.

Citation:

The X-ray structures of an octameric RNA duplex in presence of six di- and trivalent metal ions
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:1.701Å R work:0.164R free:0.197

NDB ID:

4ZCF

PDB ID:

4ZCF 

Release:

2015-07-29

Title:

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I

Classification:

Hydrolase-DNA complex

Authors:

Gupta, Y.K., Chan, S.H., Xu, S.Y., Aggarwal, A.K.

Citation:

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.
Nat Commun 6 pp.7363 - 7363 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.218R free:0.262

NDB ID:

5C0W

PDB ID:

5C0W 

Release:

2015-07-29

Title:

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Classification:

HYDROLASE/RNA

Authors:

Makino, D.L., Schuch, B., Stegmann, E., Baumgaertner, M., Basquin, C., Conti, E.

Citation:

RNA degradation paths in a 12-subunit nuclear exosome complex
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:4.6Å R work:0.271R free:0.283

NDB ID:

4YHW

PDB ID:

4YHW 

Release:

2015-07-22

Title:

Yeast Prp3 (296-469) in complex with fragment of U4/U6 di-snRNA

Classification:

SPLICING

Authors:

Liu, S., Mozaffari-Jovin, S., Wollenhaupt, J., Santos, K.F., Theuser, M., Dunin-Horkawicz, S., Fabrizio, P., Bujnicki, J.M., Luhrmann, R., Wahl, M.C.

Citation:

A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.
Elife 4 pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.25Å R work:0.248R free:0.299

NDB ID:

5BTE

PDB ID:

5BTE 

Release:

2015-07-22

Title:

Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+

Classification:

hydrolase/rna

Authors:

Wang, V.Y., Jiao, X., Kiledjian, M., Tong, L.

Citation:

Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.
Nucleic Acids Res. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.195R free:0.253

NDB ID:

4Y52

PDB ID:

4Y52 

Release:

2015-07-15

Title:

Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.

Classification:

transcription/dna/rna

Authors:

Wang, L., Zhou, Y., Xu, L., Xiao, R., Lu, X., Chen, L., Chong, J., Li, H., He, C., Fu, X.D., Wang, D.

Citation:

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Nature pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.5Å R work:0.201R free:0.232

NDB ID:

4Y7N

PDB ID:

4Y7N 

Release:

2015-07-15

Title:

The Structure Insight into 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.

Classification:

transcription/dna/rna

Authors:

Wang, L., Zhou, Y., Xu, L., Xiao, R., Lu, X., Chen, L., Chong, J., Li, H., He, C., Fu, X.D., Wang, D.

Citation:

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Nature pp. - 2015

Experiment:

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

NDB ID:

4YVI

PDB ID:

4YVI 

Release:

2015-07-15

Title:

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA

Classification:

TRANSFERASE/RNA

Authors:

Ito, T., Masuda, I., Yoshida, K., Goto-Ito, S., Sekine, S., Suh, S.W., Hou, Y.-M., Yokoyama, S.

Citation:

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.01Å R work:0.218R free:0.282

NDB ID:

4YVJ

PDB ID:

4YVJ 

Release:

2015-07-15

Title:

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36U)

Classification:

TRANSFERASE/RNA

Authors:

Ito, T., Masuda, I., Yoshida, K., Goto-Ito, S., Sekine, S., Suh, S.W., Hou, Y.-M., Yokoyama, S.

Citation:

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.199R free:0.277

NDB ID:

4YVK

PDB ID:

4YVK 

Release:

2015-07-15

Title:

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C)

Classification:

TRANSFERASE/RNA

Authors:

Ito, T., Masuda, I., Yoshida, K., Goto-Ito, S., Sekine, S., Suh, S.W., Hou, Y.-M., Yokoyama, S.

Citation:

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.002Å R work:0.218R free:0.283

NDB ID:

5BTM

PDB ID:

5BTM 

Release:

2015-07-15

Title:

Crystal structure of AUUCU repeating RNA that causes spinocerebellar ataxia type 10 (SCA10)

Classification:

RNA

Authors:

Park, H., Gonzalez, A.L., Yildirim, I., Tran, T., Lohman, J.R., Fang, P., Guo, M., Disney, M.D.

Citation:

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).
Biochemistry 54 pp.3851 - 3859 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.778Å R work:0.175R free:0.224

NDB ID:

4ZT0

PDB ID:

4ZT0 

Release:

2015-07-08

Title:

Crystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolution

Classification:

HYDROLASE/RNA

Authors:

Jiang, F., Zhou, K., Ma, L., Gressel, S., Doudna, J.A.

Citation:

A Cas9-guide RNA complex preorganized for target DNA recognition.
Science 348 pp.1477 - 1481 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.238R free:0.263

NDB ID:

4ZT9

PDB ID:

4ZT9 

Release:

2015-07-08

Title:

Nuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolution

Classification:

HYDROLASE/RNA

Authors:

Jiang, F., Zhou, K., Ma, L., Gressel, S., Doudna, J.A.

Citation:

A Cas9-guide RNA complex preorganized for target DNA recognition.
Science 348 pp.1477 - 1481 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.242R free:0.284

NDB ID:

5BUD

PDB ID:

5BUD 

Release:

2015-07-08

Title:

Crystal structure of Candida albicans Rai1 in complex with pU5-Mn2+

Classification:

hydrolase/RNA

Authors:

Wang, V.Y., Jiao, X., Kiledjian, M., Tong, L.

Citation:

Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.
Nucleic Acids Res. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.99Å R work:0.186R free:0.243

NDB ID:

5BS3

PDB ID:

5BS3 

Release:

2015-06-17

Title:

Crystal Structure of S.A. gyrase in complex with Compound 7

Classification:

Isomerase/DNA/RNA

Authors:

Singh, S.B., Kaelin, D.E., Wu, J., Miesel, L., Tan, C.M., Black, T., Nargund, R., Meinke, P.T., Olsen, D.B., Lagrutta, A., Lu, J., Patel, S., Rickert, K.W., Smith, R.F., Soisson, S., Sherer, E., Joyce, L.A., Wei, C., Peng, X., Wang, X., Fukuda, H., Kishii, R., Takei, M., Takano, H., Shibasaki, M., Yajima, M., Nishimura, A., Shibata, T., Fukuda, Y.

Citation:

Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2).
Bioorg.Med.Chem.Lett. 25 pp.1831 - 1835 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.65Å R work:0.17R free:0.212

NDB ID:

4WQ1

PDB ID:

4WQ1 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Tyr and mRNA with C-A mismatch in the first position in the A-site.

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.188R free:0.234

NDB ID:

4WQR

PDB ID:

4WQR 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch in the first position in the A-site.

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.15Å R work:0.189R free:0.231

NDB ID:

4WR6

PDB ID:

4WR6 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site.

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.204R free:0.249

NDB ID:

4WRA

PDB ID:

4WRA 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site and with antibiotic paromomycin.

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.194R free:0.248

NDB ID:

4WRO

PDB ID:

4WRO 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch in the second position in the A-site

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.193R free:0.23

NDB ID:

4WSD

PDB ID:

4WSD 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Phe and mRNA with C-A mismatch in the second position in the A-site and with antibiotic paromomycin.

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.95Å R work:0.193R free:0.234

NDB ID:

4WSM

PDB ID:

4WSM 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Leu and mRNA with G-U mismatch in the first position in the A- and P-sites

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.185

NDB ID:

4WT1

PDB ID:

4WT1 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Phe and mRNA with A-A mismatch in the second position in the A-site

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.199

NDB ID:

4WU1

PDB ID:

4WU1 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site

Classification:

ribosome

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.187R free:0.238

NDB ID:

4WZD

PDB ID:

4WZD 

Release:

2015-06-10

Title:

Complex of 70S ribosome with cognate tRNA-Tyr in the P-site

Classification:

ribosome

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.226R free:0.193

NDB ID:

4WZO

PDB ID:

4WZO 

Release:

2015-06-10

Title:

Complex of 70S ribosome with tRNA-fMet and mRNA

Classification:

RIBOSOME

Authors:

Rozov, A., Demeshkina, N., Westhof, E., Yusupov, M., Yusupova, G.

Citation:

Structural insights into the translational infidelity mechanism.
Nat Commun 6 pp.7251 - 7251 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.19R free:0.257

NDB ID:

4XCO

PDB ID:

4XCO 

Release:

2015-06-10

Title:

Signal-sequence induced conformational changes in the signal recognition particle

Classification:

RNA BINDING PROTEIN

Authors:

Hainzl, T., Sauer-Eriksson, A.E.

Citation:

Signal-sequence induced conformational changes in the signal recognition particle.
Nat Commun 6 pp.7163 - 7163 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.208R free:0.257

NDB ID:

4YOE

PDB ID:

4YOE 

Release:

2015-06-10

Title:

Structure of UP1 bound to RNA 5'-AGU-3'

Classification:

RNA Binding Protein/RNA

Authors:

Morgan, C.E., Meagher, J.L., Levengood, J.D., Delproposto, J., Rollins, C., Stuckey, J.A., Tolbert, B.S.

Citation:

The First Crystal Structure of the UP1 Domain of hnRNP A1 bound to RNA Reveals a New Look for an Old RNA Binding Protein.
J.Mol.Biol. pp. - 2015

Experiment:

X-RAY DIFFRACTION Resolution:1.92Å R work:0.185R free:0.237

NDB ID:

4Z3Q

PDB ID:

4Z3Q 

Release:

2015-06-03

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic Hygromycin A, mRNA and three tRNAs in the A, P and E sites at 2.6A resolution

Classification:

Ribosome/Antibiotic

Authors:

Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K.A., Blanchard, S.C., Steitz, T.A., Wilson, D.N.

Citation:

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
Mol.Cell 58 pp.832 - 844 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.6Å R work:0.232R free:0.282

NDB ID:

4Z3R

PDB ID:

4Z3R 

Release:

2015-06-03

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with Hygromycin-A at 3.1A resolution

Classification:

Ribosome/Antibiotic

Authors:

Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K.A., Blanchard, S.C., Steitz, T.A., Wilson, D.N.

Citation:

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
Mol.Cell 58 pp.832 - 844 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.231R free:0.283

NDB ID:

4Z3S

PDB ID:

4Z3S 

Release:

2015-06-03

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic A201A, mRNA and three tRNAs in the A, P and E sites at 2.65A resolution

Classification:

Ribosome/Antibiotic

Authors:

Polikanov, Y.S., Starosta, A.L., Juette, M.F., Altman, R.B., Terry, D.S., Lu, W., Burnett, B.J., Dinos, G., Reynolds, K.A., Blanchard, S.C., Steitz, T.A., Wilson, D.N.

Citation:

Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.
Mol.Cell 58 pp.832 - 844 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.65Å R work:0.225R free:0.27

NDB ID:

4Z8C

PDB ID:

4Z8C 

Release:

2015-05-20

Title:

Crystal structure of the Thermus thermophilus 70S ribosome bound to translation inhibitor oncocin

Classification:

ribosome/antibiotic

Authors:

Roy, R.N., Lomakin, I.B., Gagnon, M.G., Steitz, T.A.

Citation:

The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin.
Nat.Struct.Mol.Biol. 22 pp.466 - 469 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.202R free:0.247

NDB ID:

4ZER

PDB ID:

4ZER 

Release:

2015-05-20

Title:

Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Classification:

Ribosome

Authors:

Seefeldt, A.C., Nguyen, F., Antunes, S., Perebaskine, N., Graf, M., Arenz, S., Inampudi, K.K., Douat, C., Guichard, G., Wilson, D.N., Innis, C.A.

Citation:

The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.
Nat.Struct.Mol.Biol. 22 pp.470 - 475 2015

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.23R free:0.271

NDB ID:

4TUA

PDB ID:

4TUA 

Release:

2015-05-13

Title:

Crystal structure of ASL-Thr bound to Codon ACC-A on the Ribosome

Classification:

ribosome

Authors:

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

Citation:

Structural insights into translational recoding by frameshift suppressor tRNASufJ.
Rna 20 pp.1944 - 1954 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.207R free:0.251

NDB ID:

4TUB

PDB ID:

4TUB 

Release:

2015-05-13

Title:

Crystal structure of tRNA-Thr bound to Codon ACC-C on the Ribosome

Classification:

RIBOSOME

Authors:

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

Citation:

Structural insights into translational recoding by frameshift suppressor tRNASufJ.
Rna 20 pp.1944 - 1954 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.216R free:0.258

NDB ID:

4TUC

PDB ID:

4TUC 

Release:

2015-05-13

Title:

Crystal structure of ASL-SufJ bound to Codon ACC-A on the Ribosome

Classification:

RIBOSOME

Authors:

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

Citation:

Structural insights into translational recoding by frameshift suppressor tRNASufJ.
Rna 20 pp.1944 - 1954 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.214R free:0.252

NDB ID:

4TUD

PDB ID:

4TUD 

Release:

2015-05-13

Title:

Crystal structure of ASL-SufJ bound to Codon ACC-C on the Ribosome

Classification:

RIBOSOME

Authors:

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

Citation:

Structural insights into translational recoding by frameshift suppressor tRNASufJ.
Rna 20 pp.1944 - 1954 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.6Å R work:0.204R free:0.244

NDB ID:

4TUE

PDB ID:

4TUE 

Release:

2015-05-13

Title:

Crystal structure of ASL-SufJ bound to Codon ACC-U on the Ribosome

Classification:

RIBOSOME

Authors:

Fagan, C.E., Maehigashi, T., Dunkle, J.A., Miles, S.J., Dunham, C.M.

Citation:

Structural insights into translational recoding by frameshift suppressor tRNASufJ.
Rna 20 pp.1944 - 1954 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.5Å R work:0.214R free:0.249

NDB ID:

4PGY

PDB ID:

4PGY 

Release:

2015-05-06

Title:

Structure of human DNA polymerase beta complexed with a nicked DNA containing a GT at N-1 position and GC at N position

Classification:

Transferase,Lyase/DNA

Authors:

Koag, M.C., Lee, S.

Citation:

The spontaneous base substitution mechanisms of human DNA polymerase beta
To Be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.26Å R work:0.209R free:0.264

NDB ID:

4WB3

PDB ID:

4WB3 

Release:

2015-05-06

Title:

Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin

Classification:

DNA-RNA HYBRID

Authors:

Yatime, L., Maasch, C., Hoehlig, K., Klussmann, S., Andersen, G.R., Vater, A.

Citation:

Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer.
Nat Commun 6 pp.6481 - 6481 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.0Å R work:0.162R free:0.199

NDB ID:

4WZM

PDB ID:

4WZM 

Release:

2015-05-06

Title:

Mutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth Disease Virus complexed with RNA

Classification:

TRANSFERASE

Authors:

Ferrer-Orta, C., de la Higuera, I., Caridi, F., Sanchez-Aparicio, M.T., Moreno, E., Perales, C., Singh, K., Sarafianos, S.G., Sobrino, F., Domingo, E., Verdaguer, N.

Citation:

Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.
J.Virol. 89 pp.6848 - 6859 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.52Å R work:0.224R free:0.261

NDB ID:

4WZQ

PDB ID:

4WZQ 

Release:

2015-05-06

Title:

Mutant K20E of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus complexed with RNA

Classification:

TRANSFERASE

Authors:

Ferrer-Orta, C., de la Higuera, I., Caridi, F., Sanchez-Aparicio, M.T., Moreno, E., Perales, C., Singh, K., Sarafianos, S.G., Sobrino, F., Domingo, E., Verdaguer, N.

Citation:

Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.
J.Virol. 89 pp.6848 - 6859 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.8Å R work:0.249R free:0.27

NDB ID:

4X2B

PDB ID:

4X2B 

Release:

2015-05-06

Title:

K20A RNA dependent RNA polymerase mutant from Foot-and-Mouth disease Virus complexed with an RNA

Classification:

TRANSFERASE

Authors:

Ferrer-Orta, C., de la Higuera, I., Caridi, F., Sanchez-Aparicio, M.T., Moreno, E., Perales, C., Singh, K., Sarafianos, S.G., Sobrino, F., Domingo, E., Verdaguer, N.

Citation:

Multifunctionality of a picornavirus polymerase domain: nuclear localization signal and nucleotide recognition.
J.Virol. 89 pp.6848 - 6859 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.94Å R work:0.215R free:0.258

NDB ID:

4XNR

PDB ID:

4XNR 

Release:

2015-05-06

Title:

Vibrio Vulnificus Adenine Riboswitch Aptamer Domain, Synthesized by Position-selective Labeling of RNA (PLOR), in Complex with Adenine

Classification:

RNA

Authors:

Liu, Y., Holmstrom, E., Zhang, J., Yu, P., Wang, J., Dyba, M.A., Chen, D., Ying, J., Lockett, S., Nesbitt, D.J., Ferre-D'Amare, A.R., Sousa, R., Stagno, J.R., Wang, Y.X.

Citation:

Synthesis and applications of RNAs with position-selective labelling and mosaic composition.
Nature 522 pp.368 - 372 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.21Å R work:0.2R free:0.219

NDB ID:

4YCO

PDB ID:

4YCO 

Release:

2015-04-22

Title:

E. coli dihydrouridine synthase C (DusC) in complex with tRNAPhe

Classification:

OXIDOREDUCTASE

Authors:

Byrne, R.T., Jenkins, H.T., Peters, D.T., Whelan, F., Stowell, J., Aziz, N., Kasatsky, P., Rodnina, M.V., Koonin, E.V., Konevega, A.L., Antson, A.A.

Citation:

Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.
Proc.Natl.Acad.Sci.USA 112 pp.6033 - 6037 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.192R free:0.223

NDB ID:

4YCP

PDB ID:

4YCP 

Release:

2015-04-22

Title:

E. coli dihydrouridine synthase C (DusC) in complex with tRNATrp

Classification:

Oxidoreductase/RNA

Authors:

Byrne, R.T., Jenkins, H.T., Peters, D.T., Whelan, F., Stowell, J., Aziz, N., Kasatsky, P., Rodnina, M.V., Koonin, E.V., Konevega, A.L., Antson, A.A.

Citation:

Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.
Proc.Natl.Acad.Sci.USA 112 pp.6033 - 6037 2015

Experiment:

X-RAY DIFFRACTION Resolution:2.55Å R work:0.208R free:0.234

NDB ID:

4YLN

PDB ID:

4YLN 

Release:

2015-04-22

Title:

E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA

Classification:

TRANSCRIPTION/DNA/RNA

Authors:

Zuo, Y., Steitz, T.A.

Citation:

Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.
Mol.Cell 58 pp.534 - 540 2015

Experiment:

X-RAY DIFFRACTION Resolution:5.5Å R work:0.244R free:0.328