Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

4PTF
DownloadVisualize
BU of 4ptf by Molmil
Ternary crystal structure of yeast DNA polymerase epsilon with template G
Descriptor: 1,2-ETHANEDIOL, 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3', ...
Authors:Jain, R, Rajashankar, K.R, Buku, A, Johnson, R.E, Prakash, L, Prakash, S, Aggarwal, A.K.
Deposit date:2014-03-10
Release date:2014-04-30
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.809 Å)
Cite:Crystal Structure of Yeast DNA Polymerase epsilon Catalytic Domain.
Plos One, 9, 2014
2M23
DownloadVisualize
BU of 2m23 by Molmil
NMR solution structure of the d3'-hairpin of the group II intron Sc.ai5gamma including EBS1 bound to IBS1
Descriptor: RNA (29-MER), RNA_(5'-R(*CP*AP*GP*UP*GP*UP*C)-3')_
Authors:Kruschel, D, Skilandat, M, Sigel, R.K.O.
Deposit date:2012-12-12
Release date:2013-12-18
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Rna, 20, 2014
2M24
DownloadVisualize
BU of 2m24 by Molmil
NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
Descriptor: RNA (29-MER)
Authors:Kruschel, D, Skilandat, M, Sigel, R.K.O.
Deposit date:2012-12-12
Release date:2013-12-18
Last modified:2024-05-01
Method:SOLUTION NMR
Cite:NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Rna, 20, 2014
9EAL
DownloadVisualize
BU of 9eal by Molmil
SpCas9 with 17-bp R-loop containing 2 terminal mismatches (State II - precleavage)
Descriptor: CRISPR-associated endonuclease Cas9/Csn1, DNA (Non-target strand), DNA (Target Strand), ...
Authors:Kiernan, K.A, Taylor, D.W.
Deposit date:2024-11-11
Release date:2025-07-09
Method:ELECTRON MICROSCOPY (2.83 Å)
Cite:Visualization of a multi-turnover Cas9 after product release.
Nat Commun, 16, 2025
5D4D
DownloadVisualize
BU of 5d4d by Molmil
Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP
Descriptor: ADENOSINE MONOPHOSPHATE, CYTIDINE-5'-MONOPHOSPHATE, CYTIDINE-5'-TRIPHOSPHATE, ...
Authors:Zhang, Y, Ebright, R.H.
Deposit date:2015-08-07
Release date:2016-07-06
Last modified:2024-11-06
Method:X-RAY DIFFRACTION (3 Å)
Cite:The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Nature, 535, 2016
5D4C
DownloadVisualize
BU of 5d4c by Molmil
Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP
Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CYTIDINE-5'-MONOPHOSPHATE, CYTIDINE-5'-TRIPHOSPHATE, ...
Authors:Zhang, Y, Ebright, R.H.
Deposit date:2015-08-07
Release date:2016-07-06
Last modified:2024-11-20
Method:X-RAY DIFFRACTION (3.28 Å)
Cite:The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Nature, 535, 2016
8RED
DownloadVisualize
BU of 8red by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 8nt complex
Descriptor: DNA (46-MER), DNA (51-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-09
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
8RE4
DownloadVisualize
BU of 8re4 by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt pre-translocated complex
Descriptor: DNA (47-MER), DNA (50-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-09
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
8REB
DownloadVisualize
BU of 8reb by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex
Descriptor: DNA (43-MER), DNA (52-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-09
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
8REE
DownloadVisualize
BU of 8ree by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 9nt complex
Descriptor: DNA (45-MER), DNA (49-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
8REA
DownloadVisualize
BU of 8rea by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 5nt post-translocated complex
Descriptor: DNA (44-MER), DNA (51-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
8REC
DownloadVisualize
BU of 8rec by Molmil
Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 7nt complex
Descriptor: DNA (46-MER), DNA (51-MER), DNA-directed RNA polymerase subunit alpha, ...
Authors:Gao, F, Zhang, X.
Deposit date:2023-12-10
Release date:2024-01-17
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Proc.Natl.Acad.Sci.USA, 121, 2024
9Q96
DownloadVisualize
BU of 9q96 by Molmil
Cryo-EM Structure of Bacterial RNA polymerase-sigma54 transcription open complex with wild type sigma54, from RPi(-10-1)
Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ...
Authors:Gao, F, Zhang, X.
Deposit date:2025-02-26
Release date:2025-03-12
Last modified:2025-05-07
Method:ELECTRON MICROSCOPY (4.6 Å)
Cite:Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling.
Proc.Natl.Acad.Sci.USA, 122, 2025
4DHX
DownloadVisualize
BU of 4dhx by Molmil
ENY2:GANP complex
Descriptor: 80 kDa MCM3-associated protein, Enhancer of yellow 2 transcription factor homolog
Authors:Stewart, M, Jani, D.
Deposit date:2012-01-30
Release date:2012-06-13
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export.
Nucleic Acids Res., 40, 2012
5JS2
DownloadVisualize
BU of 5js2 by Molmil
Human Argonaute-2 Bound to a Modified siRNA
Descriptor: MAGNESIUM ION, PHENOL, PHOSPHATE ION, ...
Authors:Schirle, N.T, MacRae, I.J.
Deposit date:2016-05-07
Release date:2016-07-20
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (2.954 Å)
Cite:Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide.
J.Am.Chem.Soc., 138, 2016
6EUV
DownloadVisualize
BU of 6euv by Molmil
Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (VX-787)
Descriptor: (2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid, NICKEL (II) ION, Polymerase basic protein 2
Authors:Cusack, S, Lethier, M.
Deposit date:2017-10-31
Release date:2017-12-13
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors.
Nucleic Acids Res., 46, 2018
8YFQ
DownloadVisualize
BU of 8yfq by Molmil
Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex
Descriptor: 5'-3' exoribonuclease, DNA (90-mer), DNA-directed RNA polymerase subunit, ...
Authors:Murayama, Y, Yanagisawa, T, Ehara, H, Sekine, S.
Deposit date:2024-02-25
Release date:2024-09-25
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.
Nat Commun, 15, 2024
8YFR
DownloadVisualize
BU of 8yfr by Molmil
Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft
Descriptor: 5'-3' exoribonuclease, DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ...
Authors:Murayama, Y, Yanagisawa, T, Ehara, H, Sekine, S.
Deposit date:2024-02-25
Release date:2024-09-25
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.
Nat Commun, 15, 2024
7F0R
DownloadVisualize
BU of 7f0r by Molmil
Cryo-EM structure of Pseudomonas aeruginosa SutA transcription activation complex
Descriptor: DNA (70-MER), DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, ...
Authors:He, D.W, You, L.L, Zhang, Y.
Deposit date:2021-06-06
Release date:2022-07-27
Last modified:2024-06-12
Method:ELECTRON MICROSCOPY (5.8 Å)
Cite:Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding.
Nat Commun, 13, 2022
6Z6L
DownloadVisualize
BU of 6z6l by Molmil
Cryo-EM structure of human CCDC124 bound to 80S ribosomes
Descriptor: 18S rRNA, 28S rRNA, 40S ribosomal protein S10, ...
Authors:Wells, J.N, Buschauer, R, Mackens-Kiani, T, Best, K, Kratzat, H, Berninghausen, O, Becker, T, Cheng, J, Beckmann, R.
Deposit date:2020-05-28
Release date:2020-07-29
Last modified:2024-05-22
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.
Plos Biol., 18, 2020
5FZ5
DownloadVisualize
BU of 5fz5 by Molmil
Transcription initiation complex structures elucidate DNA opening (CC)
Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2, ...
Authors:Plaschka, C, Hantsche, M, Dienemann, C, Burzinski, C, Plitzko, J, Cramer, P.
Deposit date:2016-03-10
Release date:2016-05-18
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (8.8 Å)
Cite:Transcription Initiation Complex Structures Elucidate DNA Opening
Nature, 533, 2016
5FYW
DownloadVisualize
BU of 5fyw by Molmil
Transcription initiation complex structures elucidate DNA opening (OC)
Descriptor: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2, ...
Authors:Plaschka, C, Hantsche, M, Dienemann, C, Burzinski, C, Plitzko, J, Cramer, P.
Deposit date:2016-03-10
Release date:2016-05-18
Last modified:2024-05-08
Method:ELECTRON MICROSCOPY (4.35 Å)
Cite:Transcription Initiation Complex Structures Elucidate DNA Opening
Nature, 533, 2016
4CGV
DownloadVisualize
BU of 4cgv by Molmil
First TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD
Descriptor: GLYCEROL, HEAT SHOCK PROTEIN HSP 90-ALPHA, RNA POLYMERASE II-ASSOCIATED PROTEIN 3
Authors:Roe, S.M, Pal, M.
Deposit date:2013-11-26
Release date:2014-05-14
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.54 Å)
Cite:Structural Basis for Phosphorylation-Dependent Recruitment of Tel2 to Hsp90 by Pih1.
Structure, 22, 2014
4CGW
DownloadVisualize
BU of 4cgw by Molmil
Second TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD
Descriptor: HEAT SHOCK PROTEIN HSP 90-ALPHA, RNA POLYMERASE II-ASSOCIATED PROTEIN 3
Authors:Roe, S.M, Pal, M.
Deposit date:2013-11-26
Release date:2014-05-14
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (3.001 Å)
Cite:Structural Basis for Phosphorylation-Dependent Recruitment of Tel2 to Hsp90 by Pih1.
Structure, 22, 2014
8JDJ
DownloadVisualize
BU of 8jdj by Molmil
Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)
Descriptor: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
Authors:Ishiguro, K, Yokoyama, T, Shirouzu, M, Suzuki, T.
Deposit date:2023-05-14
Release date:2023-12-06
Last modified:2025-02-12
Method:ELECTRON MICROSCOPY (2.5 Å)
Cite:Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth.
Cell, 186, 2023

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon