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As of 23-Jul-2014 number of released structures: 7272
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Polymer Type: All + RNA Type: All + Protein Function: All + Experimental Method: All + RNA Sequence Type: All RNA Sequence

Results: 2809   (Gallery view)

NDB ID:

2MKI

PDB ID:

2MKI 

Release:

2014-07-23

Title:

Solution structure of tandem RRM domains of cytoplasmic polyadenylation element binding protein 4 (CPEB4) in complex with RNA

Classification:

TRANSLATION REGULATOR/RNA

Authors:

Afroz, T., Skrisovska, L., Belloc, E., Guillen-Boixet, J., Mendez, R., Allain, F.H.-T.

Citation:

A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins
Genes Dev. 28 pp.1498 - 1514 2014

Experiment:

SOLUTION NMR

NDB ID:

2MKK

PDB ID:

2MKK 

Release:

2014-07-23

Title:

Structural model of tandem RRM domains of cytoplasmic polyadenylation element binding protein 1 (CPEB1) in complex with RNA

Classification:

TRANSLATION REGULATOR/RNA

Authors:

Afroz, T., Skrisovska, L., Belloc, E., Guillen-Boixet, J., Mendez, R., Allain, F.H.-T.

Citation:

A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins
Genes Dev. 28 pp.1498 - 1514 2014

Experiment:

SOLUTION NMR

NDB ID:

NA2902

PDB ID:

4OJI 

Release:

2014-07-23

Title:

Crystal Structure of Twister Ribozyme

Classification:

RNA

Authors:

Liu, Y., Wilson, T.J., McPhee, S.A., Lilley, D.M.J.

Citation:

Crystal structure and mechanistic investigation of the twister ribozyme
NAT.CHEM.BIOL. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.3Å R work:0.179R free:0.202

NDB ID:

NA3048

PDB ID:

4QOZ 

Release:

2014-07-23

Title:

Crystal structure of the histone mRNA stem-loop, stem-loop binding protein (phosphorylated), and 3'hExo ternary complex

Classification:

RNA/HYDROLASE/RNA BINDING PROTEIN

Authors:

Zhang, J., Tan, D., DeRose, E.F., Perera, L., Dominski, Z., Marzluff, W.F., Tong, L., Hall, T.M.

Citation:

Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation.
Proc.Natl.Acad.Sci.USA pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.304Å R work:0.193R free:0.245

NDB ID:

NA3068

PDB ID:

4UN3 

Release:

2014-07-23

Title:

Crystal structure of Cas9 bound to PAM-containing DNA target

Classification:

HYDROLASE/DNA/RNA

Authors:

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

Citation:

Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease
Nature pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.593Å R work:0.217R free:0.252

NDB ID:

NA3069

PDB ID:

4UN4 

Release:

2014-07-23

Title:

Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2

Classification:

HYDROLASE/DNA/RNA

Authors:

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

Citation:

Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease
Nature pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.371Å R work:0.216R free:0.248

NDB ID:

NA3070

PDB ID:

4UN5 

Release:

2014-07-23

Title:

Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at positions 1-3

Classification:

HYDROLASE/DNA/RNA

Authors:

Anders, C., Niewoehner, O., Duerst, A., Jinek, M.

Citation:

Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease
Nature pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.4Å R work:0.214R free:0.246

NDB ID:

NA2601

PDB ID:

4LMZ 

Release:

2014-07-16

Title:

Structural insight into RNA recognition by RRM1+2 domain of human ETR-3 protein

Classification:

RNA BINDING PROTEIN

Authors:

Bhatt, H., Manickam, Y., Bhavesh, N.S.

Citation:

sequence specific RNA recognition of ETR3 RRM 1-2 domains
TO BE PUBLISHED pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:2.78Å R work:0.244R free:0.292

Equivalence Class: 

NR_all_06529.1 

Eq. Class Rep:

4LMZ

NDB ID:

NA2639

PDB ID:

4LX5 

Release:

2014-07-16

Title:

X-ray crystal structure of the M6"" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)

Classification:

RNA

Authors:

Robinson, C.J., Vincent, H.A., Wu, M.C., Lowe, P.T., Dunstan, M.S., Leys, D., Micklefield, J.

Citation:

Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species.
J.Am.Chem.Soc. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.13Å R work:0.199R free:0.256

Equivalence Class: 

NR_all_53611.1 

Eq. Class Rep:

4LX6

NDB ID:

NA2682

PDB ID:

4LX6 

Release:

2014-07-16

Title:

X-ray crystal structure of the M6C"" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO)

Classification:

RNA

Authors:

Robinson, C.J., Vincent, H.A., Wu, M.C., Lowe, P.T., Dunstan, M.S., Leys, D., Micklefield, J.

Citation:

Modular Riboswitch Toolsets for Synthetic Genetic Control in Diverse Bacterial Species.
J.Am.Chem.Soc. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.15Å R work:0.203R free:0.254

Equivalence Class: 

NR_all_53611.1 

Eq. Class Rep:

4LX6

NDB ID:

NA3023

PDB ID:

4QI2 

Release:

2014-07-16

Title:

X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Schlundt, A., Heinz, G.A., Janowski, R., Geerlof, A., Stehle, R., Heissmeyer, V., Niessing, D., Sattler, M.

Citation:

Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation
Nat.Struct.Mol.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.203R free:0.246

Equivalence Class: 

NR_all_61164.1 

Eq. Class Rep:

4QI2

NDB ID:

NA3038

PDB ID:

4QIK 

Release:

2014-07-16

Title:

Crystal structure of the ROQ domain of human Roquin in complex with the TNF23 RNA duplex

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Tan, D., Zhou, M., Kiledjian, M., Tong, L.

Citation:

The ROQ domain of Roquin recognizes mRNA constitutive decay element and double-stranded RNA
Nat.Struct.Mol.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.177R free:0.211

Equivalence Class: 

NR_all_34596.1 

Eq. Class Rep:

4QIK

NDB ID:

NA3039

PDB ID:

4QIL 

Release:

2014-07-16

Title:

Crystal structure of the ROQ domain of human Roquin in complex with the Hmg19 stem-loop RNA

Classification:

RNA BINDING PROTEIN/RNA

Authors:

Tan, D., Zhou, M., Kiledjian, M., Tong, L.

Citation:

The ROQ domain of Roquin recognizes mRNA constitutive decay element and double-stranded RNA
Nat.Struct.Mol.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.194R free:0.25

Equivalence Class: 

NR_all_02064.1 

Eq. Class Rep:

4QIL

NDB ID:

NA2832

PDB ID:

4O41 

Release:

2014-07-09

Title:

Amide linked RNA

Classification:

RNA

Authors:

Mutisya, D., Selvam, C., Lunstad, B.D., Pallan, P.S., Haas, A., Leake, D., Egli, M., Rozners, E.

Citation:

Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.
Nucleic Acids Res. 42 pp.6542 - 6551 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.2Å R work:0.146R free:0.211

Equivalence Class: 

NR_all_66927.1 

Eq. Class Rep:

4O41

NDB ID:

NA2982

PDB ID:

4Q5S 

Release:

2014-07-09

Title:

RPase in complex with DNA and RNA

Classification:

transcription/DNA/rna

Authors:

Basu, R.S., Warner, B.A., Molodtsov, V., Pupov, D., Esyunina, D., Fernandez-Tornero, C., Kulbachinskiy, A., Murakami, K.

Citation:

Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme
J.Biol.Chem. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.269R free:0.293

Equivalence Class: 

NR_all_06068.1 

Eq. Class Rep:

4Q5S

NDB ID:

NA2510

PDB ID:

4LF4 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

RIBOSOME

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
To be Published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.3421Å R work:0.171R free:0.207

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2511

PDB ID:

4LF5 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
To be Published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.753Å R work:0.163R free:0.218

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2512

PDB ID:

4LF6 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
To be Published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.3052Å R work:0.175R free:0.21

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2513

PDB ID:

4LF7 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
To be Published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.1484Å R work:0.168R free:0.205

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2514

PDB ID:

4LF8 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
to be published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.1484Å R work:0.168R free:0.205

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2515

PDB ID:

4LF9 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
to be published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.2811Å R work:0.168R free:0.201

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2516

PDB ID:

4LFA 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
to be published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.6461Å R work:0.153R free:0.204

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2535

PDB ID:

4LFB 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

RIBOSOME

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus
to be published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.009Å R work:0.169R free:0.203

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2536

PDB ID:

4LFC 

Release:

2014-07-02

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Classification:

ribosome

Authors:

Demirci, H., Belardinelli, R., Carr, J., Murphy IV, F., Jogl, G., Dahlberg, A.E., Gregory, S.T.

Citation:


to be published pp. - 2013

Experiment:

X-RAY DIFFRACTION Resolution:3.602Å R work:0.162R free:0.208

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2783

PDB ID:

4NFO 

Release:

2014-07-02

Title:

Crystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC

Classification:

RNA

Authors:

Phelps, K.J., Ibarra-Soza, J.M., Tran, K., Fisher, A.J., Beal, P.A.

Citation:

Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.
Acs Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.96Å R work:0.217R free:0.241

Equivalence Class: 

NR_all_51063.1 

Eq. Class Rep:

4NFO

NDB ID:

NA2784

PDB ID:

4NFP 

Release:

2014-07-02

Title:

Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 8-aza-7-deaza-7-ethynyl Adenosine

Classification:

RNA

Authors:

Phelps, K.J., Ibarra-Soza, J.M., Tran, K., Fisher, A.J., Beal, P.A.

Citation:

Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.
Acs Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.85Å R work:0.222R free:0.249

Equivalence Class: 

NR_all_51063.1 

Eq. Class Rep:

4NFO

NDB ID:

NA2785

PDB ID:

4NFQ 

Release:

2014-07-02

Title:

Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 7-triazolyl-8-aza-7-deazaadenosine

Classification:

RNA

Authors:

Phelps, K.J., Ibarra-Soza, J.M., Tran, K., Fisher, A.J., Beal, P.A.

Citation:

Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.
Acs Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.7Å R work:0.222R free:0.243

Equivalence Class: 

NR_all_51063.1 

Eq. Class Rep:

4NFO

NDB ID:

NA2898

PDB ID:

4OO1 

Release:

2014-07-02

Title:

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

Classification:

HYDROLASE/RNA

Authors:

Wasmuth, E.V., Januszyk, K., Lima, C.D.

Citation:

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA
Nature pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.226R free:0.264

Equivalence Class: 

NR_all_53316.1 

Eq. Class Rep:

4OO1

NDB ID:

NA3044

PDB ID:

4CQN 

Release:

2014-07-02

Title:

Crystal structure of the E.coli LeuRS-tRNA complex with the non- cognate isoleucyl adenylate analogue

Classification:

LIGASE/RNA

Authors:

Cvetesic, N., Palencia, A., Halasz, I., Cusack, S., Gruic-Sovulj, I.

Citation:

The Physiological Target for Leurs Translational Quality Control is Norvaline
Embo J. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.5Å R work:0.213R free:0.29

Equivalence Class: 

NR_all_79796.4 

Eq. Class Rep:

4AQ7

NDB ID:

NA2470

PDB ID:

4KZD 

Release:

2014-06-18

Title:

Crystal structure of an RNA aptamer in complex with fluorophore and Fab

Classification:

immune system/rna

Authors:

Huang, H., Suslov, N.B., Li, N.S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Citation:

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.186Å R work:0.179R free:0.21

Equivalence Class: 

NR_all_71787.1 

Eq. Class Rep:

4KZD

NDB ID:

NA2471

PDB ID:

4KZE 

Release:

2014-06-18

Title:

Crystal structure of an RNA aptamer in complex with Fab

Classification:

immune system/rna

Authors:

Huang, H., Suslov, N.B., Li, N.S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Citation:

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.404Å R work:0.186R free:0.223

Equivalence Class: 

NR_all_71787.1 

Eq. Class Rep:

4KZD

NDB ID:

NA2917

PDB ID:

3WQY 

Release:

2014-06-18

Title:

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with wild-type tRNA(Ala) having G3.U70

Classification:

LIGASE/RNA

Authors:

Naganuma, M., Sekine, S., Chong, Y.E., Guo, M., Yang, X.L., Gamper, H., Hou, Y.M., Schimmel, P., Yokoyama, S.

Citation:

The selective tRNA aminoacylation mechanism based on a single G.U pair
Nature 510 pp.507 - 511 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.25R free:0.289

Equivalence Class: 

NR_all_16209.1 

Eq. Class Rep:

3WQY

NDB ID:

NA2918

PDB ID:

3WQZ 

Release:

2014-06-18

Title:

Crystal structure of Archaeoglobus fulgidus alanyl-tRNA synthetase in complex with a tRNA(Ala) variant having A3.U70

Classification:

LIGASE/RNA

Authors:

Naganuma, M., Sekine, S., Chong, Y.E., Guo, M., Yang, X.L., Gamper, H., Hou, Y.M., Schimmel, P., Yokoyama, S.

Citation:

The selective tRNA aminoacylation mechanism based on a single G.U pair
Nature 510 pp.507 - 511 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.489Å R work:0.241R free:0.276

Equivalence Class: 

NR_all_16209.1 

Eq. Class Rep:

3WQY

NDB ID:

NA2944

PDB ID:

4PQU 

Release:

2014-06-18

Title:

Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP

Classification:

TRANSFERASE, HYDROLASE/DNA/RNA

Authors:

Das, K., Martinez, S.E., Bandwar, R.P., Arnold, E.

Citation:

Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Nucleic Acids Res. 42 pp.8125 - 8137 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.508Å R work:0.201R free:0.265

Equivalence Class: 

NR_all_59142.1 

Eq. Class Rep:

4PQU

NDB ID:

NA2959

PDB ID:

4PUO 

Release:

2014-06-18

Title:

Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and Nevirapine

Classification:

TRANSFERASE, HYDROLASE/DNA/RNA/INHIBITOR

Authors:

Das, K., Martinez, S.E., Bandwar, R.P., Arnold, E.

Citation:

Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Nucleic Acids Res. 42 pp.8125 - 8137 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.901Å R work:0.228R free:0.285

Equivalence Class: 

NR_all_59142.1 

Eq. Class Rep:

4PQU

NDB ID:

NA2963

PDB ID:

4PWD 

Release:

2014-06-18

Title:

Crystal structure of HIV-1 reverse transcriptase in complex with bulge-RNA/DNA and Nevirapine

Classification:

TRANSFERASE, HYDROLASE/DNA/RNA/INHIBITOR

Authors:

Das, K., Martinez, S.E., Bandwar, R.P., Arnold, E.

Citation:

Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Nucleic Acids Res. 42 pp.8125 - 8137 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.0Å R work:0.221R free:0.29

Equivalence Class: 

NR_all_59142.1 

Eq. Class Rep:

4PQU

NDB ID:

NA2975

PDB ID:

4Q0B 

Release:

2014-06-18

Title:

Crystal structure of HIV-1 reverse transcriptase in complex with gap-RNA/DNA and Nevirapine

Classification:

TRANSFERASE, HYDROLASE/RNA/DNA/INHIBITOR

Authors:

Das, K., Martinez, S.E., Bandwar, R.P., Arnold, E.

Citation:

Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage.
Nucleic Acids Res. 42 pp.8125 - 8137 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.3Å R work:0.234R free:0.317

Equivalence Class: 

NR_all_66380.1 

Eq. Class Rep:

4Q0B

NDB ID:

NA2990

PDB ID:

4Q9Q 

Release:

2014-06-18

Title:

Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab

Classification:

RNA

Authors:

Huang, H., Suslov, N.B., Li, N.S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Citation:

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.45Å R work:0.181R free:0.22

Equivalence Class: 

NR_all_71787.1 

Eq. Class Rep:

4KZD

NDB ID:

NA2991

PDB ID:

4Q9R 

Release:

2014-06-18

Title:

Crystal structure of an RNA aptamer bound to trifluoroethyl-ligand analog in complex with Fab

Classification:

RNA/immune system

Authors:

Huang, H., Suslov, N.B., Li, N.S., Shelke, S.A., Evans, M.E., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Citation:

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Nat.Chem.Biol. pp. - 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.12Å R work:0.202R free:0.253

Equivalence Class: 

NR_all_71787.1 

Eq. Class Rep:

4KZD

NDB ID:

NA3034

PDB ID:

4D25 

Release:

2014-06-18

Title:

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA and AMPPNP

Classification:

HYDROLASE

Authors:

Xiol, J., Spinelli, P., Laussmann, M.A., Homolka, D., Yang, Z., Cora, E., Coute, Y., Conn, S., Kadlec, J., Sachidanandam, R., Kaksonen, M., Cusack, S., Ephrussi, A., Pillai, R.S.

Citation:

RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts.
Cell(Cambridge,Mass.) 157 pp.1698 - 2014

Experiment:

X-RAY DIFFRACTION Resolution:1.9Å R work:0.171R free:0.208

Equivalence Class: 

NR_all_45463.1 

Eq. Class Rep:

4D25

NDB ID:

NA3035

PDB ID:

4D26 

Release:

2014-06-18

Title:

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi

Classification:

HYDROLASE

Authors:

Xiol, J., Spinelli, P., Laussmann, M.A., Homolka, D., Yang, Z., Cora, E., Coute, Y., Conn, S., Kadlec, J., Sachidanandam, R., Kaksonen, M., Cusack, S., Ephrussi, A., Pillai, R.S.

Citation:

RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts.
Cell(Cambridge,Mass.) 157 pp.1698 - 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.1Å R work:0.224R free:0.277

Equivalence Class: 

NR_all_45463.1 

Eq. Class Rep:

4D25

NDB ID:

2M1V

PDB ID:

2M1V 

Release:

2014-06-11

Title:

NMR solution structure of the d3'-hairpin from the Sc.ai5gamma group II intron including the EBS1:dIBS1 RNA:DNA hybrid

Classification:

DNA/RNA

Authors:

Skilandat, M., Sigel, R.K.

Citation:

The Role of Magnesium(II) for DNA Cleavage Site Recognition in Group II Intron Ribozymes -- Solution Structure and Metal Ion Binding Sites of the RNADNA Complex.
J.Biol.Chem. pp. - 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_13624.1 

Eq. Class Rep:

2M23

NDB ID:

NA2482

PDB ID:

4KVB 

Release:

2014-06-04

Title:

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

Classification:

RIBOSOME

Authors:

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

Citation:

Structural robustness of the ribosome inferred from the X-ray crystal structure of a 30S ribosomal subunit lacking ribosomal protein S17
To be Published pp. - 0

Experiment:

X-RAY DIFFRACTION Resolution:4.198Å R work:0.217R free:0.257

Equivalence Class: 

NR_all_42982.28 

Eq. Class Rep:

1FJG

NDB ID:

NA2826

PDB ID:

4NYA 

Release:

2014-06-04

Title:

Crystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine

Classification:

RNA

Authors:

Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Citation:

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Chem.Biol. 21 pp.591 - 595 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.65Å R work:0.225R free:0.273

Equivalence Class: 

NR_all_11749.1 

Eq. Class Rep:

2GDI

NDB ID:

NA2827

PDB ID:

4NYB 

Release:

2014-06-04

Title:

Crystal structure of the E. coli thiM riboswitch in complex with (4-(1,2,3-thiadiazol-4-yl)phenyl)methanamine

Classification:

RNA

Authors:

Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Citation:

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Chem.Biol. 21 pp.591 - 595 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.1Å R work:0.188R free:0.248

Equivalence Class: 

NR_all_57109.1 

Eq. Class Rep:

2HOJ

NDB ID:

NA2828

PDB ID:

4NYC 

Release:

2014-06-04

Title:

Crystal structure of the E. coli thiM riboswitch in complex with thieno[2,3-b]pyrazin-7-amine

Classification:

RNA

Authors:

Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Citation:

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Chem.Biol. 21 pp.591 - 595 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.15Å R work:0.201R free:0.263

Equivalence Class: 

NR_all_57109.1 

Eq. Class Rep:

2HOJ

NDB ID:

NA2829

PDB ID:

4NYD 

Release:

2014-06-04

Title:

Crystal structure of the E. coli thiM riboswitch in complex with hypoxanthine

Classification:

RNA

Authors:

Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Citation:

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Chem.Biol. 21 pp.591 - 595 2014

Experiment:

X-RAY DIFFRACTION Resolution:2.9Å R work:0.199R free:0.257

Equivalence Class: 

NR_all_57109.1 

Eq. Class Rep:

2HOJ

NDB ID:

NA2830

PDB ID:

4NYG 

Release:

2014-06-04

Title:

Crystal structure of the E. coli thiM riboswitch in complex with thiamine

Classification:

RNA

Authors:

Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., Ferre-D'Amare, A.R.

Citation:

Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Chem.Biol. 21 pp.591 - 595 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.05Å R work:0.248R free:0.322

Equivalence Class: 

NR_all_57109.1 

Eq. Class Rep:

2HOJ

NDB ID:

NA2938

PDB ID:

4OQU 

Release:

2014-06-04

Title:

Structure of the SAM-I/IV riboswitch (env87(deltaU92))

Classification:

RNA

Authors:

Trausch, J.J., Xu, Z., Edwards, A.L., Reyes, F.E., Ross, P.E., Knight, R., Batey, R.T.

Citation:

Structural basis for diversity in the SAM clan of riboswitches.
Proc.Natl.Acad.Sci.USA 111 pp.6624 - 6629 2014

Experiment:

X-RAY DIFFRACTION Resolution:3.2Å R work:0.195R free:0.226

Equivalence Class: 

NR_all_03769.1 

Eq. Class Rep:

4L81

NDB ID:

2MJH

PDB ID:

2MJH 

Release:

2014-05-28

Title:

Solution structure of the GLD-1 RNA-binding domain in complex with RNA

Classification:

RNA BINDING PROTEIN

Authors:

Daubner, G.M., Brummer, A., Tocchini, C., Gerhardy, S., Ciosk, R., Zavolan, M., Allain, F.H.

Citation:

Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.
Nucleic Acids Res. pp. - 2014

Experiment:

SOLUTION NMR

Equivalence Class: 

NR_all_35462.1 

Eq. Class Rep:

2MJH