[English] 日本語
Yorodumi
- PDB-6bqf: Pol II elongation complex with 'dT-AP' at i+1, i-1 position -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bqf
TitlePol II elongation complex with 'dT-AP' at i+1, i-1 position
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
  • RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
KeywordsTRANSFERASE/TRANSCRIPTION / Complex / DNA BINDING PROTEIN / DNA-RNA HYBRID / TRANSCRIPTION / TRANSFERASE-TRANSCRIPTION complex
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 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / termination of RNA polymerase II transcription / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / termination of RNA polymerase II transcription / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / 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 / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase III transcription / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / : / : / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / Gyrase A; domain 2 - #140 / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / Homeodomain-like / 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. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / 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. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / 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 polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit
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 (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.35 Å
AuthorsWang, W. / Wang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102362 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Authors: Wang, W. / Walmacq, C. / Chong, J. / Kashlev, M. / Wang, D.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
T: DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')
R: RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,86321
Polymers481,31512
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61210 Å2
ΔGint-394 kcal/mol
Surface area136090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.400, 221.350, 193.700
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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

#1: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB2, RPB150, RPO22, YOR151C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB3, YIL021W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370
#7: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB9, YGL070C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999
#9: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB11, YOL005C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902

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

#4: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#5: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#6: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436
#8: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139
#10: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

-
DNA chain / RNA chain , 2 types, 2 molecules TR

#11: DNA chain DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3')


Mass: 8770.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: RNA chain RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')


Mass: 2918.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 9 molecules

#13: Chemical
ChemComp-ZN / ZINC ION


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


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 9-12% PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→82.8 Å / Num. obs: 92041 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 6.5
Reflection shellResolution: 3.35→3.53 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.35→82.763 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2446 4549 4.94 %
Rwork0.2171 --
obs0.2184 92012 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.35→82.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27808 426 9 0 28243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228794
X-RAY DIFFRACTIONf_angle_d0.53438969
X-RAY DIFFRACTIONf_dihedral_angle_d11.37310984
X-RAY DIFFRACTIONf_chiral_restr0.0214383
X-RAY DIFFRACTIONf_plane_restr0.0024970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3501-3.38810.414340.3045749X-RAY DIFFRACTION23
3.3881-3.4280.2876740.28621404X-RAY DIFFRACTION45
3.428-3.46980.3042940.3031873X-RAY DIFFRACTION59
3.4698-3.51370.29411180.29522165X-RAY DIFFRACTION69
3.5137-3.560.35491220.29132537X-RAY DIFFRACTION80
3.56-3.60870.32331630.29662795X-RAY DIFFRACTION90
3.6087-3.66030.29571560.28713186X-RAY DIFFRACTION99
3.6603-3.71490.30331630.27463121X-RAY DIFFRACTION100
3.7149-3.7730.32841490.27063202X-RAY DIFFRACTION100
3.773-3.83480.29231850.26133105X-RAY DIFFRACTION100
3.8348-3.9010.26941340.25973172X-RAY DIFFRACTION100
3.901-3.97190.26891580.25183215X-RAY DIFFRACTION100
3.9719-4.04830.26061750.2283114X-RAY DIFFRACTION100
4.0483-4.13090.26071600.22373159X-RAY DIFFRACTION100
4.1309-4.22070.24941680.20933202X-RAY DIFFRACTION100
4.2207-4.31890.25861550.20173162X-RAY DIFFRACTION100
4.3189-4.42690.2131640.19683126X-RAY DIFFRACTION100
4.4269-4.54660.22491660.1913170X-RAY DIFFRACTION100
4.5466-4.68040.2191700.18373167X-RAY DIFFRACTION100
4.6804-4.83140.21451720.17973176X-RAY DIFFRACTION100
4.8314-5.00410.23961530.18983165X-RAY DIFFRACTION100
5.0041-5.20440.23011700.18683141X-RAY DIFFRACTION100
5.2044-5.44120.2371730.19713183X-RAY DIFFRACTION100
5.4412-5.7280.20991550.20123147X-RAY DIFFRACTION100
5.728-6.08680.23211790.20973169X-RAY DIFFRACTION100
6.0868-6.55660.24821590.21573154X-RAY DIFFRACTION99
6.5566-7.21610.23751660.19853148X-RAY DIFFRACTION99
7.2161-8.25940.18771710.183170X-RAY DIFFRACTION99
8.2594-10.40280.16311560.15113181X-RAY DIFFRACTION99
10.4028-82.78840.22021870.20413205X-RAY DIFFRACTION99
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)
10.03790.0119-0.01030.0057-0.00120.01290.0467-0.02980.13150.0581-0.0820.1791-0.0333-0.1386-0.01520.05280.1627-0.04960.309-0.08650.4921288.090734.1579438.1063
20.00050.0784-0.03020.0538-0.00780.36710.2729-0.1153-0.3474-0.09330.10680.01740.38610.05060.74340.10120.20760.0315-0.2747-0.1974-0.1144333.472613.6051423.4628
30.06440.0480.05630.05270.01240.0670.06340.0713-0.0994-0.12120.09950.00810.3296-0.01880.12310.5428-0.0781-0.31660.0309-0.09090.3528312.909-11.0783412.3268
4-0.0025-0.00040.00540.0240.02380.01940.03390.01780.05890.0035-0.0305-0.00130.058-0.00820.00090.80550.0113-0.21320.19530.12250.4121305.74235.8261370.4081
50.11720.04540.06290.05140.00790.0553-0.0497-0.04150.1079-0.1902-0.01120.13990.0069-0.0784-0.07430.2265-0.1009-0.20060.12860.04770.3176303.972913.6198410.7963
60.009-0.00430.0060.0239-0.02330.0310.0842-0.06880.1393-0.08320.0370.0461-0.13560.01420.10350.31080.14240.19960.0594-0.14230.2196329.876964.982430.2053
70.07450.0101-0.00410.0260.00220.01010.0381-0.03840.1715-0.08420.04350.128-0.1103-0.07770.12640.18340.25510.1630.1770.00630.2576312.370761.2708410.0567
80.0369-0.0124-0.03260.0243-0.04530.11710.02930.00260.0777-0.0621-0.01360.0165-0.10530.1450.01060.2380.03620.25420.14670.00560.085339.977159.3689407.181
90.0133-0.02570.04690.0227-0.03530.05640.0853-0.10240.00410.178-0.0040.0552-0.0615-0.02680.06790.02040.07350.28840.126-0.2555-0.0765333.628940.3615451.0498
100.020.02210.0570.1380.03930.12260.025-0.08480.039-0.0298-0.03270.22940.117-0.07710.007-0.11830.14980.08120.2963-0.15530.2972323.551123.6434438.4551
110.0031-0.00240.00020.001-0.0002-0-0.0060.00390.00140.0053-0.0093-0.00070.01040.0112-00.230.146-0.08740.4405-0.02770.398375.520410.8997445.8929
120.02140.0155-0.02010.0126-0.01690.023-0.01250.0089-0.05380.004-0.0217-0.0150.02250.0288-0.00740.19390.1116-0.11490.3783-0.08250.277358.640717.9547454.0698
130.00490.0055-0.00170.0034-0.00380.00510.0143-0.00560.00010.0127-0.0022-0.0060.01620.03560.0217-0.0059-0.0016-0.0030.182-0.05910.075355.790231.7756461.1139
140.01330.00590.00090.0157-0.00280.00150.0179-0.04120.01650.02910.0371-0.01630.02670.05990.03940.1127-0.0476-0.12690.3308-0.04110.1437360.00437.6311464.0388
150.00610.0083-0.00820.00780.00410.00680.02390.0526-0.0177-0.0385-0.0245-0.06520.02870.0607-0.00230.18030.10130.00930.3234-0.10170.2562364.761614.2441432.7512
160.00780.00010.0030.00950.00450.00130.04740.0041-0.02540.01840.0335-0.04810.05050.01730.01330.2270.1786-0.08120.34790.03790.2744365.75465.3203447.4739
170.00310.00170.0019-0.00010.00090.00270.00810.0329-0.0123-0.0176-0.0077-0.02920.0065-0.0035-00.6568-0.1605-0.34660.56750.05860.5708290.36834.8445377.0702
180.00260.00270.00250.00160.00130.0014-0.00260.01190.01330.0042-0.01980.00520.0084-0.011100.7334-0.0962-0.17610.7114-0.00460.7571280.2045-1.7518386.1315
190.00260.00120.00170.0004-0.00040.00030.00880.0095-0.0036-0.00350.00140.0027-0.0134-0.001900.9291-0.0257-0.07670.99190.06241.013278.1847.8672386.1662
200.0026-0.00020.00150.00020.00050.00050.01440.00630.0135-0.0039-0.001-0.004-0.02220.0044-00.9019-0.0219-0.0740.97690.09911.0326273.724314.2065388.1507
210.00540.00130.00140.00370.00760.0143-0.0241-0.01850.0189-0.014-0.0510.0680.0059-0.0667-0.02730.3089-0.1804-0.26050.2156-0.00680.4556290.1533.8119404.5418
22-0.00010.00020.00030.0008-0.00020.00030.0030.0014-0.0034-0.00770.0115-0.00940.00740.0026-00.4592-0.0632-0.03830.44750.04240.5084294.5024-11.0117432.357
230.00080.0005-0.00080.0008-0.00060.00090.0118-0.0215-0.0067-0.0019-0.00630.00790.0043-0.002400.3168-0.07240.00260.3293-0.01560.3021306.4545-1.9527446.2667
240-0.00010.00020.0005-00.0006-0.0078-0.0042-0.00470.004-0.01030.00470.00330.001-00.7366-0.0441-0.070.701-0.02690.7092312.4862-9.8861456.4675
250-00.00030.0004-0.00040.00110.00050.0022-0.00550.00260.0054-0.00470.00050.001200.5237-0.09390.01360.40150.02010.4426309.594-10.1467448.4043
260.0035-0.00150.00110.002-0.00060.00030.0014-0.00130.0009-0.00030.00210.0020.00450.003600.4506-0.0093-0.0070.45270.01340.4474294.7088-4.1805437.7706
270.00050.00020.00020.0006-0.00060.00020.00980.00390.0020.00170.00020.00180.0029-0.007500.5725-0.06590.00220.60740.03050.6797291.7258-5.4207433.4842
280.00270.0007-0.00120.0008-0.00050.00090.005-0.0049-0.001-0.0040.0112-0.00490.0060.00400.4213-0.0415-0.04750.36960.02630.4359305.6136-12.8065437.6403
290.0008-0.0016-0.00160.0012-0.00010.0006-0.01150.0147-0.00180.0014-0.0033-0.00210.00870.011600.75910.11860.0610.645-0.11150.7744358.3457-21.6017410.7064
300.0001-0.0003-0.00090.0006-0.00010.0013-0.0175-0.00040.0131-0.0073-0.0026-0.00420.00430.0058-00.48810.1631-0.0040.4693-0.08430.5141356.2843-7.0923410.9575
310.0018-0.00070.00160.00110.00090.001-0.00860.01320.0046-0.00340.0093-0.00150.0032-0.006300.52660.12890.00390.4961-0.11290.5614355.8289-20.5239407.3384
320.0012-0.0011-0.00060.00110.00170.004-0.010.00260.0037-0.0010.0074-0.0109-0.00080.001-00.4160.1025-0.02210.4622-0.07240.4472364.805-10.7627413.7998
330.0006-0.00220.00050.0019-0.0010.00040.00010.0023-0.013-0.0135-0.0093-0.00430.00650.007100.57020.08040.00710.4319-0.10420.5282355.3557-22.1423427.3965
34-0-0.0006-0.00040.00040.0010.00190.0042-0.0087-0.0025-0.0039-0.00260.00030.00040.0013-00.76780.07650.0140.74270.02790.7847362.7351-24.2639433.7826
350.0004-0.0015-0.00060.00290.00260.00080.0009-0.00680.00500.0079-0.01010.0076-0.0018-00.5960.0303-0.02730.5043-0.24410.5784349.841-19.6614417.4158
360.0015-0.00170.00060.00130.00090.0007-0.0077-0.00420.00710.00810.0051-0.0066-0.00530.000600.57330.0609-0.0250.497-0.08820.5605345.3105-23.0833408.5684
370.0007-0.00090.00080.00170.00050.0017-0.0016-0.00230.0020.00450.00950.0042-0.0014-0.0079-00.60690.0907-0.0540.5385-0.05880.5294349.2971-17.1392411.6813
38-0.00020-00.0004-0.00020.00010.0052-0.0052-0.00570.00130.00180-0.0029-0.004100.75150.0088-0.00150.678-0.05010.7142345.958-27.7252416.7036
390.0032-0.0003-0.00130.00060.00030.0003-0.00290.00320.00130.0032-0.01180.003600.008500.65050.05780.02540.5975-0.04950.6409361.0461-21.7132419.5036
400.0005-0.00020.0020.00640.00120.00230.01650.0241-0.0196-0.00830.02110.0072-0.0118-0.0259-00.63980.0477-0.15030.31990.16490.4751303.189162.7263371.5371
410.00410.00770.00070.0109-0.00030.00030.03010.01350.0013-0.00230.0144-0.00310.0225-0.00330.03860.248-0.0170.10020.31750.02180.1022335.697150.839381.8999
420.00110.0016-0.00160.0011-0.00160.00020.0328-0.0017-0.00670.00210.02370-0.01320.007300.157-0.01850.06180.3683-0.0730.2903359.452434.1132446.653
430.001-0.0004-0.00040.0004-0.00030.0009-0.0086-0.00530.0030.002-0.0057-0.0006-0.00470.0023-00.236-0.03740.08510.3283-0.06360.314367.137445.5082441.97
440.00140.00240.00150.00660.00370.00210.00010.00060.00220.0004-0.0027-0.0013-0.00420.001800.5355-0.01320.0130.58670.0210.5779373.207346.975435.8844
450.00120.0003-0.0004-0.0001-0.0002-0.0002-0.0160.004-0.00130.0026-0.00750.0014-0.00130.0114-00.1683-0.01130.12230.3030.04280.2678369.15435.2239437.6462
46-0.0002-0.00030.00010.00140.0006-0.00020.0138-0.0067-0.00940.00270.0011-0.0126-0.01650.004300.16480.050.09740.2948-0.04280.1609358.681536.7628438.7941
470.0008-0.00010.00010.0004-0.00020.00010.00180.00310.00840.00760.0045-0.0059-0.00160.001100.1496-0.02840.06950.223-0.0240.2274350.656954.2027448.8391
480.0009-0.00190.00550.0009-0.00050.00310.052-0.0333-0.0049-0.00540.00540.01320.03260.0382-00.2550.0634-0.05250.2710.03850.2292344.47062.9499455.8315
490.0008-0.00160.00090.00350.00160.0001-0.0079-0.0104-0.008-0.005-0.0074-0.01220.00050.0075-0.00080.19550.1173-0.04930.17880.01370.2419358.5207-4.3911446.9549
500.004-0.00270.00450.0050.00310.00650.0023-0.0147-0.023-0.0012-0.0118-0.00680.01460.0121-0.00320.22710.1034-0.17790.19550.07040.1974348.4128-4.7692448.2386
510.0043-0.00630.00290.0059-0.0051-0.00070.0415-0.01270-0.00250.0599-0.01470.04910.046200.34230.1398-0.05540.53030.07520.553370.71023.0669454.051
520.00040.0006-0.0010.0008-0.00090.00130.00490.0038-0.0004-0.0087-0.0025-0.005700.001700.72040.0007-0.00570.7072-0.06750.7065339.117559.0262463.9665
530.0383-0.0008-0.009200.00030.003700.0003-0.0019-00.0013-0.00150.00010.00010.00010.7666-0.01040.00810.7231-0.08030.7451336.219660.2108470.3433
540.01740.0184-0.02660.0197-0.02830.0408-0.002-0.00030.0011-0.0006-0.0004-0.0001-0.00020.0008-01.52330.0109-0.00331.5262-0.01591.5232326.789161.1851469.3878
55-0.0008-0.0026-0.00150.00150.00350.00170.0022-0.0020.0054-0.00350.00020.0068-0.03440.0438-00.25080.01020.05720.3032-0.10430.1603339.718750.9886463.5703
56-0.00070.0019-0.0003-0.0005-0.00050.0002-0.0375-0.00780.00520.019-0.011-0.0176-0.0040.0219-00.99510.03010.03291.04680.110.9927315.658639.5231438.276
570.0004-0.00010.00070.0010.00130.0013-0.0026-0.00470.02080.00450.00120.0209-0.0261-0.0075-01.1597-0.0958-0.02451.13920.05091.1739318.227739.447435.8486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 394 )
2X-RAY DIFFRACTION2chain 'A' and (resid 395 through 844 )
3X-RAY DIFFRACTION3chain 'A' and (resid 845 through 1116 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1117 through 1280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1281 through 1446 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 241 )
7X-RAY DIFFRACTION7chain 'B' and (resid 242 through 533 )
8X-RAY DIFFRACTION8chain 'B' and (resid 534 through 776 )
9X-RAY DIFFRACTION9chain 'B' and (resid 777 through 994 )
10X-RAY DIFFRACTION10chain 'B' and (resid 995 through 1220 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 26 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 51 )
13X-RAY DIFFRACTION13chain 'C' and (resid 52 through 84 )
14X-RAY DIFFRACTION14chain 'C' and (resid 85 through 162 )
15X-RAY DIFFRACTION15chain 'C' and (resid 163 through 209 )
16X-RAY DIFFRACTION16chain 'C' and (resid 210 through 268 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3 through 54 )
18X-RAY DIFFRACTION18chain 'E' and (resid 55 through 71 )
19X-RAY DIFFRACTION19chain 'E' and (resid 72 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 72 through 86 )
23X-RAY DIFFRACTION23chain 'F' and (resid 87 through 103 )
24X-RAY DIFFRACTION24chain 'F' and (resid 104 through 116 )
25X-RAY DIFFRACTION25chain 'F' and (resid 117 through 132 )
26X-RAY DIFFRACTION26chain 'F' and (resid 133 through 137 )
27X-RAY DIFFRACTION27chain 'F' and (resid 138 through 147 )
28X-RAY DIFFRACTION28chain 'F' and (resid 148 through 155 )
29X-RAY DIFFRACTION29chain 'H' and (resid 3 through 16 )
30X-RAY DIFFRACTION30chain 'H' and (resid 17 through 30 )
31X-RAY DIFFRACTION31chain 'H' and (resid 31 through 43 )
32X-RAY DIFFRACTION32chain 'H' and (resid 44 through 53 )
33X-RAY DIFFRACTION33chain 'H' and (resid 54 through 82 )
34X-RAY DIFFRACTION34chain 'H' and (resid 83 through 92 )
35X-RAY DIFFRACTION35chain 'H' and (resid 93 through 106 )
36X-RAY DIFFRACTION36chain 'H' and (resid 107 through 118 )
37X-RAY DIFFRACTION37chain 'H' and (resid 119 through 127 )
38X-RAY DIFFRACTION38chain 'H' and (resid 128 through 140 )
39X-RAY DIFFRACTION39chain 'H' and (resid 141 through 146 )
40X-RAY DIFFRACTION40chain 'I' and (resid 2 through 52 )
41X-RAY DIFFRACTION41chain 'I' and (resid 53 through 116 )
42X-RAY DIFFRACTION42chain 'J' and (resid 1 through 17 )
43X-RAY DIFFRACTION43chain 'J' and (resid 18 through 26 )
44X-RAY DIFFRACTION44chain 'J' and (resid 27 through 31 )
45X-RAY DIFFRACTION45chain 'J' and (resid 32 through 43 )
46X-RAY DIFFRACTION46chain 'J' and (resid 44 through 56 )
47X-RAY DIFFRACTION47chain 'J' and (resid 57 through 65 )
48X-RAY DIFFRACTION48chain 'K' and (resid 1 through 39 )
49X-RAY DIFFRACTION49chain 'K' and (resid 40 through 55 )
50X-RAY DIFFRACTION50chain 'K' and (resid 56 through 82 )
51X-RAY DIFFRACTION51chain 'K' and (resid 83 through 114 )
52X-RAY DIFFRACTION52chain 'L' and (resid 27 through 36 )
53X-RAY DIFFRACTION53chain 'L' and (resid 37 through 41 )
54X-RAY DIFFRACTION54chain 'L' and (resid 42 through 46 )
55X-RAY DIFFRACTION55chain 'L' and (resid 47 through 70 )
56X-RAY DIFFRACTION56chain 'T' and (resid 18 through 29 )
57X-RAY DIFFRACTION57chain 'R' and (resid 1 through 9 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more