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- PDB-9pvu: RNA polymerase II elongation complex with dC at +1 site, 8-oxo-GM... -

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Basic information

Entry
Database: PDB / ID: 9pvu
TitleRNA polymerase II elongation complex with dC at +1 site, 8-oxo-GMP added.
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • Non-template strand DNA
  • RNA with 8-oxo-guanine added to 3' end
  • Template strand DNA
KeywordsTRANSCRIPTION / RNA polymerase II / oxidative damage / in vitro transcription / 8-oxoguanine
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / Dual incision in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase III / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / translesion synthesis / DNA-templated transcription elongation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / transcription by RNA polymerase II / ribonucleoside binding / cytoplasmic stress granule / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / metal ion binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon ...: / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb1, domain 1 / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsHou, P. / Oh, J. / Wang, D.
Funding support United States, Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM147652 United States
National Research Foundation (NRF, Korea)RS-2024-00344054 Korea, Republic Of
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotides.
Authors: Peini Hou / Chanjoo Lee / Jenny Chong / Juntaek Oh / Dong Wang /
Abstract: Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription ...Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription fidelity are poorly understood. Here, we investigate the structural basis of transcription-coupled RNA damage and the effect of 8-oxo-guanosine triphosphate (8-oxo-rGTP) on RNA polymerase II (Pol II) transcription fidelity control steps. We revealed that the incorporation efficiency of 8-oxo-rGTP opposite a dC template is comparable to that of GTP. In contrast, the incorporation efficiency of 8-oxo-rGTP opposite a dA template is ~150-fold more efficient than that of GTP. For the extension step, Pol II extends substantially faster from a 3'-8-oxo-rG:dC base pair than from a 3'-8-oxo-rG:dA base pair. For the proofreading step, strikingly, Pol II EC with 3'-8-oxo-rG:dA base pair is much more resistant to backtracking and proofreading than Pol II EC with 3'-8-oxo-rG:dC base pair. Using X-ray crystallography, we revealed that 8-oxo-rGTP adopts different prechemistry binding sites depending on whether it is paired with a dC or a dA template. Upon incorporation, the nucleobase of 8-oxo-rG flips to the -conformation to form a Hoogsteen pair with a dA template, whereas it remains in the -conformation to form a Watson-Crick pair with a dC template. Collectively, our work demonstrates that nucleotide-pool oxidation can directly affect Pol II fidelity control steps and elongation dynamics and induce RNA damage in a transcription-coupled manner.
History
DepositionAug 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: RNA with 8-oxo-guanine added to 3' end
T: Template strand DNA
N: Non-template strand DNA
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,83322
Polymers487,28513
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.999, 223.510, 192.778
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA with 8-oxo-guanine added to 3' end


Mass: 3296.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 2 types, 2 molecules TN

#2: DNA chain Template strand DNA


Mass: 8699.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Non-template strand DNA


Mass: 5663.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

#4: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB2, RPB150, RPO22, YOR151C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB3, YIL021W / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P16370
#10: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB9, YGL070C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P27999
#12: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB11, YOL005C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20434
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20435
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20436
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22139
#13: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40422

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.31→49.32 Å / Num. obs: 102682 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 91.57 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.481 / Net I/σ(I): 5.2
Reflection shellResolution: 3.31→3.37 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5031 / CC1/2: 0.231

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.31→49.32 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 1998 1.95 %
Rwork0.2434 --
obs0.2441 102309 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28007 1012 9 0 29028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329653
X-RAY DIFFRACTIONf_angle_d0.60540278
X-RAY DIFFRACTIONf_dihedral_angle_d17.59411341
X-RAY DIFFRACTIONf_chiral_restr0.0424545
X-RAY DIFFRACTIONf_plane_restr0.0045042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.390.43781380.46942X-RAY DIFFRACTION97
3.39-3.480.43881410.36867089X-RAY DIFFRACTION99
3.48-3.590.36661420.33617146X-RAY DIFFRACTION100
3.59-3.70.3121420.31277160X-RAY DIFFRACTION100
3.7-3.840.34151430.37199X-RAY DIFFRACTION100
3.84-3.990.30971430.28447149X-RAY DIFFRACTION100
3.99-4.170.32161430.24697172X-RAY DIFFRACTION100
4.17-4.390.25461420.22177165X-RAY DIFFRACTION100
4.39-4.660.26391450.21027198X-RAY DIFFRACTION100
4.66-5.020.25471420.21177185X-RAY DIFFRACTION100
5.02-5.530.30271440.22747209X-RAY DIFFRACTION100
5.53-6.330.27521440.23797198X-RAY DIFFRACTION100
6.33-7.970.27261440.22067229X-RAY DIFFRACTION100
7.97-49.320.19771450.1887270X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0092-0.00460.0080.00720.00110.0044-0.01740.0207-0.01420.0452-0.0421-0.04030.03560.0466-00.73320.0950.23990.60980.0960.938513.302313.00239.564
20.0297-0.0008-0.03040.0086-0.00080.02-0.04230.12390.0357-0.12030.06910.01550.0929-0.092700.7681-0.0848-0.18150.9188-0.02230.942344.151611.060469.2455
30.00990.0076-0.00060.00420.00560.0059-0.2076-0.0277-0.0397-0.0443-0.18020.0356-0.04960.0204-0.00010.6593-0.19150.09090.4621-0.03790.586913.494411.042936.6424
40.00080.00330.0041-0.00060.00550.0019-0.14540.0154-0.0818-0.0491-0.1838-0.03560.06740.0091-0.00041.4496-0.28190.17191.51-0.33181.482744.98310.599872.7193
50.1661-0.0318-0.08360.0596-0.05520.07860.09820.17990.4306-0.2626-0.0484-0.42140.0740.4267-0.00510.7426-0.2891-0.28941.21050.21391.37453.51989.520639.8761
60.10940.0110.2204-0.0252-0.18170.11670.07590.07610.170.13250.1196-0.02490.23710.14630.10440.5378-0.0466-0.16980.27770.04120.367311.739-12.014733.0475
70.4482-0.0847-0.25920.5197-0.03140.22290.1966-0.3123-0.07760.30450.0579-0.08550.4628-0.01990.26720.8104-0.1547-0.09280.33620.15710.3258-4.6423-8.584765.2743
80.19670.0950.1030.13810.07170.47140.018-0.0716-0.0640.43330.1391-0.05940.23780.3010.61061.01960.0791-0.40750.10870.11240.305123.9403-18.359274.3685
90.0369-0.04660.02180.08010.02890.0650.0448-0.03250.25630.18270.0021-0.0613-0.1815-0.024700.5226-0.04340.05890.42450.05790.53520.632941.672240.5771
100.0618-0.0070.0170.0097-0.00590.0309-0.03410.0360.03760.01970.1495-0.04710.02740.0603-0.00020.8461-0.0133-0.03950.294-0.01850.513821.262229.603171.1511
110.0566-0.0110.0180.03190.03320.04630.1204-0.00730.07220.4540.0597-0.1406-0.0681-0.02870.01420.555-0.0785-0.01840.3316-0.05080.458122.151739.143864.9875
120.10140.00070.04820.15960.04080.08220.09660.03670.04390.06070.0449-0.0842-0.0386-0.30970.10980.11780.07910.2960.3990.05360.381-6.600129.701563.6219
130.08160.02240.12230.06330.08390.1659-0.1580.1562-0.114-0.04580.00130.0661-0.06990.01-0.1087-0.2902-0.19940.41630.50910.12080.3428-8.97587.193932.3359
140.0168-0.0677-0.04680.10470.09020.10370.03350.1875-0.08480.2844-0.1682-0.07220.09620.186-0.06520.44160.0117-0.18140.59680.18010.582732.9493-4.258328.705
150.09440.02720.08710.01830.02830.0763-0.05590.0193-0.0688-0.0591-0.05640.029-0.0223-0.1162-0.05850.1273-0.26930.04940.61130.0790.5404-35.4383-13.00726.1034
160.01790.00160.0141-0.00220.00910.0296-0.1376-0.0046-0.02-0.04870.02510.01850.1191-0.0201-0.02930.3112-0.12120.09290.62980.12780.2488-23.95393.809510.9551
170.13480.0435-0.04310.1201-0.00420.06480.15850.025-0.09360.0212-0.06980.00760.2175-0.19730.00270.4496-0.0976-0.01830.60830.06670.4419-32.2324-7.269828.4803
180.00930.0030.00160.0036-0.00330.00460.09320.0107-0.0154-0.0089-0.08-0.00090.0380.07301.0588-0.0254-0.28470.78420.03180.916842.0411-18.418693.9787
190.0303-0.01150.01010.00870.00620.0133-0.08360.0414-0.06730.13320.01850.0046-0.08960.0733-01.22910.2988-0.33891.2523-0.11971.002350.5717-22.782793.8189
200.00360.00370.00390.00290.00290.00730.0361-0.05130.02650.0015-0.022-0.0350.02090.031801.1009-0.1164-0.25611.2508-0.29811.217259.6013-11.558585.3987
21-0.0062-0.01570.02210.00330.0140.0688-0.1014-0.11890.03650.1084-0.05130.0237-0.0524-0.1575-0.13760.66730.172-0.48830.4075-0.0230.485942.5475-22.751370.4515
220.06630.0688-0.00430.110.00080.0010.0107-0.0125-0.0034-0.00460.0129-0.0028-0.009-0.0027-0.00011.5120.05530.00871.51740.02821.513951.1965-30.497939.7932
230.00560.00320.00560.00410.00590.004-0.02010.0778-0.03580.10110.01920.05250.0106-0.037400.61450.17370.01540.7448-0.05810.630629.5346-33.252336.2265
240.0020.0015-0.00270.0014-0.00030.0036-0.04260.05480.0018-0.011-0.0352-0.04230.03880.01-0.00010.70240.0017-0.06440.7012-0.06220.675419.5058-35.858219.487
250.005-0.0031-0.00930.00450.01130.01790.1113-0.0239-0.0014-0.0156-0.0061-0.0118-0.03140.00570.00010.73220.11040.00440.7019-0.01410.581230.0138-35.682434.8314
260.00290.005-0.00240.0046-0.00230.00280.0495-0.04740.00190.0240.00520.02970.0397-0.004101.1146-0.20780.18030.85830.40271.0916-26.0028-49.236264.8323
270.0052-0.00020.0060.0050.00690.0107-0.0025-0.0251-0.0599-0.0010.0008-0.00750.0026-0.0034-00.9539-0.3017-0.01530.69260.17070.8491-26.2229-39.923165.5547
280.0262-0.0127-0.01820.00840.00990.0125-0.0445-0.02660.0143-0.0479-0.0495-0.03030.0181-0.0183-00.9478-0.17260.00240.79650.18220.9394-27.7389-50.338661.1185
290.00090.0017-0.00250.00140.00270.00240.02280.0686-0.02370.0005-0.01330.00770.05270.0218-01.027-0.2914-0.02410.84020.04411.0316-25.9262-49.843441.9799
300.00150.004-0.00270.0109-0.00280.0043-0.02430.0009-0.02750.06890.01790.07020.0627-0.00900.9019-0.17170.05320.76120.40180.9065-16.0928-47.11662.697
310.0014-0.0006-0.00070.00150.00190.00390.00930.0016-0.01170.0009-0.0010.0145-0.00140.0046-01.54670.0140.00681.60080.07711.63-16.2661-58.105366.4131
320.0016-0.0028-0.00030.004-0.00110.0022-0.0015-0.0070.00260.0634-0.00370.00630.004-0.0138-01.065-0.12940.0330.97320.12821.0961-20.7136-50.649155.6912
330.008-0.0060.00780.0192-0.00030.0026-0.00820.0328-0.09570.1-0.0209-0.0146-0.03460.0409-01.0981-0.0667-0.00880.5875-0.14620.645128.91437.1572103.3261
340.0005-0.0019-0.0030.0217-0.00420.00760.0321-0.078-0.0050.0064-0.0665-0.04170.0296-0.0925-01.016-0.01640.00040.80610.01980.5984-2.781324.217493.7895
350.20570.1190.11390.07340.0640.0646-0.01960.01680.13570.0003-0.19350.0913-0.0223-0.0113-0.08650.433-0.02850.26920.55670.05520.354-31.585312.129131.576
360.0506-0.0004-0.02290.0501-0.01980.0070.0156-0.02510.01410.017-0.03470.01580.0631-0.06610.02030.1598-0.01630.33140.79330.07520.5974-28.800314.476635.1967
370.03450.01740.01760.01050.00910.009-0.0221-0.0011-0.00420.0012-0.0162-0.02350.0178-0.024100.577-0.0158-0.07920.6870.01730.7951-5.2616-6.372121.5307
380.004-0.0022-0.00110.0022-0.00020.0012-0.01210.0035-0.00130.0013-0.0228-0.00890.0034-0.0022-0.00010.629-0.09550.03910.70370.05440.5656-14.6435-11.452118.3981
390.0015-0.00230.0042-0.00010.0012-0.00010.23160.0805-0.0065-0.0640.0855-0.0896-0.0527-0.00310.00020.5215-0.05290.02320.6634-0.10620.6549-13.4616-30.13520.4462
400.005-0.00410.00420.0028-0.0040.0027-0.03840.0168-0.01270.0338-0.01740.030.0163-0.0196-0.00010.4597-0.0732-0.18150.46810.07560.7574-25.6671-28.46729.0647
410.0209-0.02160.01390.0145-0.01070.00980.08390.0436-0.0376-0.03030.02690.042-0.0902-0.03300.6135-0.0527-0.18190.6042-0.01810.6487-17.3841-29.080729.7714
420.0035-0.0029-0.00180.00290.00130.00060.0280.06560.0633-0.0038-0.0146-0.04960.0196-0.0181-0.00010.4207-0.1820.0460.532-0.14490.7229-16.2206-32.676326.803
430.01290.0169-0.01150.0184-0.0134-0.00540.0630.0573-0.0666-0.02270.0883-0.04570.0786-0.15280.00010.5912-0.30530.01740.8784-0.04860.8903-36.6065-27.103722.572
440.0007-0.0001-0.00070.00010.00030.0010.0187-0.03610.01850.02060.00090.0381-0.0046-0.007101.37230.0503-0.06171.2282-0.00631.3498-7.845232.580110.9724
450.00150.0020.00030.0032-0.00250.0039-0.00410.00260.015-0.01910.0248-0.0161-0.0113-0.01750.00012.16440.00730.10942.25320.16732.0733-1.702337.08679.2294
460.0023-0.00280.00340.0055-0.00780.0101-0.11630.0226-0.08250.0423-0.0711-0.0091-0.0228-0.0132-01.1853-0.0362-0.18831.08950.05351.0048-5.38424.810110.7241
470.00010.0023-0.00190.0064-0.00540.0046-0.0016-0.0145-0.0081-0.01030.03510.0102-0.00130.0126-00.6994-0.05430.01630.71620.08570.6363-14.19316.319813.0409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'T' and (resid 4 through 18 )
3X-RAY DIFFRACTION3chain 'T' and (resid 19 through 28 )
4X-RAY DIFFRACTION4chain 'N' and (resid 2 through 15 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 282 )
6X-RAY DIFFRACTION6chain 'A' and (resid 283 through 573 )
7X-RAY DIFFRACTION7chain 'A' and (resid 574 through 845 )
8X-RAY DIFFRACTION8chain 'A' and (resid 846 through 1446 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 212 )
10X-RAY DIFFRACTION10chain 'B' and (resid 213 through 271 )
11X-RAY DIFFRACTION11chain 'B' and (resid 272 through 487 )
12X-RAY DIFFRACTION12chain 'B' and (resid 488 through 796 )
13X-RAY DIFFRACTION13chain 'B' and (resid 797 through 1094 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1095 through 1221 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 51 )
16X-RAY DIFFRACTION16chain 'C' and (resid 52 through 104 )
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 268 )
18X-RAY DIFFRACTION18chain 'E' and (resid 4 through 26 )
19X-RAY DIFFRACTION19chain 'E' and (resid 27 through 89 )
20X-RAY DIFFRACTION20chain 'E' and (resid 90 through 130 )
21X-RAY DIFFRACTION21chain 'E' and (resid 131 through 215 )
22X-RAY DIFFRACTION22chain 'F' and (resid 69 through 73 )
23X-RAY DIFFRACTION23chain 'F' and (resid 74 through 102 )
24X-RAY DIFFRACTION24chain 'F' and (resid 103 through 116 )
25X-RAY DIFFRACTION25chain 'F' and (resid 117 through 154 )
26X-RAY DIFFRACTION26chain 'H' and (resid 2 through 16 )
27X-RAY DIFFRACTION27chain 'H' and (resid 17 through 53 )
28X-RAY DIFFRACTION28chain 'H' and (resid 54 through 60 )
29X-RAY DIFFRACTION29chain 'H' and (resid 61 through 92 )
30X-RAY DIFFRACTION30chain 'H' and (resid 93 through 126 )
31X-RAY DIFFRACTION31chain 'H' and (resid 127 through 133 )
32X-RAY DIFFRACTION32chain 'H' and (resid 134 through 146 )
33X-RAY DIFFRACTION33chain 'I' and (resid 2 through 52 )
34X-RAY DIFFRACTION34chain 'I' and (resid 53 through 119 )
35X-RAY DIFFRACTION35chain 'J' and (resid 1 through 28 )
36X-RAY DIFFRACTION36chain 'J' and (resid 29 through 65 )
37X-RAY DIFFRACTION37chain 'K' and (resid 1 through 5 )
38X-RAY DIFFRACTION38chain 'K' and (resid 6 through 10 )
39X-RAY DIFFRACTION39chain 'K' and (resid 11 through 39 )
40X-RAY DIFFRACTION40chain 'K' and (resid 40 through 52 )
41X-RAY DIFFRACTION41chain 'K' and (resid 53 through 69 )
42X-RAY DIFFRACTION42chain 'K' and (resid 70 through 77 )
43X-RAY DIFFRACTION43chain 'K' and (resid 78 through 114 )
44X-RAY DIFFRACTION44chain 'L' and (resid 28 through 38 )
45X-RAY DIFFRACTION45chain 'L' and (resid 39 through 53 )
46X-RAY DIFFRACTION46chain 'L' and (resid 54 through 63 )
47X-RAY DIFFRACTION47chain 'L' and (resid 64 through 70 )

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