[English] 日本語
Yorodumi
- PDB-6nhg: Rhodobacter sphaeroides Mitochondrial respiratory chain complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nhg
TitleRhodobacter sphaeroides Mitochondrial respiratory chain complex
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer
Function / homology
Function and homology information


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / Chem-AZO / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial ...1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / Chem-AZO / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXia, D. / Zhou, F. / Esser, L.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit.
Authors: Esser, L. / Zhou, F. / Yu, C.A. / Xia, D.
History
DepositionDec 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,14723
Polymers241,13311
Non-polymers9,01412
Water61334
1
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
hetero molecules

A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)500,29346
Polymers482,26622
Non-polymers18,02724
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area110240 Å2
ΔGint-719 kcal/mol
Surface area161620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.181, 154.181, 598.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

-
Cytochrome b-c1 complex subunit ... , 9 types, 9 molecules ABEFGHIJK

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 49266.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P31800
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 46575.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23004
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13370.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00129
#7: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9448.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13271
#8: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 9189.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00126
#9: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 7964.259 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Amino terminal signal peptide of mitiochondrial bc1 Rieske protein
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: UQCRFS1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7338.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00130
#11: Protein Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 6396.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07552

-
Protein , 2 types, 2 molecules CD

#3: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42620.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00157
#4: Protein Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CYC1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P00125

-
Non-polymers , 9 types, 46 molecules

#12: Chemical ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 410.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H33NO8P
#13: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#14: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#15: Chemical ChemComp-AZO / METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE / AZOXYSTROBIN


Mass: 403.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17N3O5
#16: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#17: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#18: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#19: Chemical ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM MOPS 7.2 pH, 20 mM Ammonium acetate, 20% glycerol. Incubation with 2-5 mol excess of Azoxystrobin. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57
Temp details: constant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.739 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 3, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 167324 / % possible obs: 99.8 % / Redundancy: 23.2 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.022 / Rrim(I) all: 0.107 / Χ2: 1.009 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8515.21.18943920.8890.311.230.824100
2.85-2.924.81.40943990.9440.2871.4390.846100
2.9-2.9625.61.07344030.9650.2151.0950.757100
2.96-3.0225.60.90244090.9770.1810.920.702100
3.02-3.0825.50.83144180.9790.1670.8480.75100
3.08-3.1525.50.52844300.9850.1060.5390.786100
3.15-3.2325.30.4444110.9890.0890.4490.847100
3.23-3.3225.10.31144210.9940.0630.3170.92100
3.32-3.4224.90.2644470.9950.0530.2650.975100
3.42-3.5324.80.20244270.9960.0410.2071.055100
3.53-3.6523.70.16844220.9970.0350.1721.192100
3.65-3.823.40.16444580.9960.0340.1681.48399.9
3.8-3.9722.90.11844580.9980.0250.121.25699.8
3.97-4.1822.30.09844440.9980.0210.11.21199.8
4.18-4.4421.70.08144600.9990.0170.0831.2399.5
4.44-4.7821.30.07344540.9990.0160.0741.16799.2
4.78-5.2621.30.06544850.9990.0140.0671.17799.5
5.26-6.0221.80.06745500.9990.0140.0681.09299.9
6.02-7.5621.80.05745860.9990.0120.0591.02699.9
7.56-3021.80.04447400.9990.0090.0450.98898.1

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQX

1sqx


Resolution: 2.8→29.87 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.44
RfactorNum. reflection% reflection
Rfree0.289 3731 2.23 %
Rwork0.251 --
obs0.2518 167324 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 270.33 Å2 / Biso mean: 108.8564 Å2 / Biso min: 37.99 Å2
Refinement stepCycle: final / Resolution: 2.8→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16342 0 1002 34 17378
Biso mean--120.53 57.78 -
Num. residues----2080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.83540.31591400.322961146254100
2.8354-2.87270.34211360.328761346270100
2.8727-2.9120.44571410.34156063620499
2.912-2.95360.42131370.35546058619599
2.9536-2.99760.48091400.36746030617099
2.9976-3.04440.42761340.36246030616498
3.0444-3.09430.40021440.35286045618998
3.0943-3.14760.35431360.33526094623099
3.1476-3.20480.34361360.32815983611998
3.2048-3.26630.44051330.33475959609297
3.2663-3.33290.42911360.29746051618798
3.3329-3.40530.37991320.31246018615098
3.4053-3.48440.28921360.28986051618799
3.4844-3.57140.3261400.27116082622299
3.5714-3.66780.36841410.27356048618999
3.6678-3.77550.31221420.26885997613998
3.7755-3.89710.28921420.23966042618499
3.8971-4.03610.26311430.24276074621799
4.0361-4.19730.27491340.23426057619199
4.1973-4.38770.23871400.22136053619399
4.3877-4.61830.21851410.19816056619799
4.6183-4.90640.26551410.1966081622299
4.9064-5.28340.2351330.2046117625099
5.2834-5.81150.2841440.239261036247100
5.8115-6.64440.27961360.253161396275100
6.6444-8.34090.26911350.222261126247100
8.3409-29.87170.21881380.22636002614097
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)
10.7385-0.29030.37170.7432-0.46741.3030.08420.0003-0.0261-0.0779-0.00620.56430.1101-0.6475-00.7447-0.17860.03820.87630.01311.235832.922687.418193.7297
20.47440.37360.31280.67110.2460.98270.0034-0.23910.18420.1562-0.11590.5570.1728-0.7026-0.05190.8464-0.32730.21360.9099-0.00431.146135.54783.9542110.9342
30.84170.04140.35441.4002-0.08550.89610.1025-0.21270.24770.3767-0.10430.2245-0.2151-0.4642-0.03870.9566-0.16780.21710.6373-0.00950.970749.550595.6846116.0338
41.38660.2894-0.15830.946-0.28021.8710.0967-0.0160.2030.13840.02670.0391-0.2428-0.1349-0.0070.847-0.13850.05090.3418-0.00440.74568.3328104.383793.5497
51.0036-0.73860.38560.99480.42671.21620.0277-0.10720.1028-0.1847-0.03690.1784-0.2003-0.1603-0.00220.8994-0.0876-0.03850.4125-0.00370.884162.546289.185577.6415
60.84240.00860.24451.613-0.10661.67110.1050.1365-0.086-0.4965-0.0680.46720.0683-0.16590.02090.8267-0.1203-0.12080.39750.01860.881956.174887.204973.6295
70.2734-0.05020.09770.250.21550.21930.0977-0.53841.01410.4739-0.30070.0271-0.74220.1341-0.01111.4705-0.50990.1121.036-0.00861.244663.325976.2264136.5706
80.99870.367-0.10921.32880.10990.52130.3327-0.6194-0.14780.8563-0.2461-0.0280.1053-0.07390.94741.6681-0.65520.07090.97980.0640.791667.489564.456161.93
90.0029-0.00460.00360.0074-0.00210.0044-0.0684-0.1965-0.29690.0248-0.11630.16430.0634-0.2274-0.00012.0134-0.64580.08921.4025-0.11250.73568.200970.6513167.0221
100.0241-0.01960.02110.0236-0.01340.07420.01110.2691-0.15780.2715-0.12770.1250.0417-0.2382-0.00031.21-0.4340.02620.68440.02720.823466.138463.661145.9768
110.74390.2946-0.21340.706-0.46750.46460.1877-0.3178-0.0620.4072-0.1092-0.05280.36810.0310.68181.4413-0.6531-0.01710.75040.23140.926464.074843.9847150.7454
120.55450.75390.22891.01430.41070.53780.1723-0.4851-0.14330.1165-0.1558-0.2930.4350.0850.4572.2095-0.80460.52351.86820.11951.119544.840160.0146181.911
130.20220.1223-0.17760.0809-0.11420.1876-0.1936-0.3288-0.10660.2409-0.01810.1240.01510.0614-0.16682.6402-0.69150.58921.872-0.0861.012746.366774.9024194.4292
140.24040.01870.04940.00040.01050.01790.3846-0.89880.15690.2676-0.02150.1345-0.1787-0.2126-0.19662.6872-0.90970.4741.9469-0.05970.85455.181373.6421193.1274
150.0773-0.0805-0.01370.15190.07410.0348-0.1662-0.27370.54890.68670.2955-0.10050.0141-0.0285-0.00012.6219-0.56620.22031.8992-0.28781.184563.927687.3492200.9066
160.5111-1.1218-0.112.47720.25170.0289-0.1516-0.3327-0.0081.15940.1769-0.07890.02280.01150.01452.5828-0.87880.28311.76440.16910.932859.279166.3859192.8053
170.0386-0.16260.12840.7358-0.59540.4923-0.1166-0.1999-0.2150.5576-0.2121-0.15730.23180.19740.19212.6562-1.08540.2222.21730.48121.286452.453147.1963199.879
180.1336-0.07810.12970.0291-0.05090.10410.1559-0.7172-0.02980.5099-0.03280.0789-0.246-0.2827-0.46992.5991-0.90420.72482.01560.17011.011246.166962.4617198.9855
190.3782-0.32880.13620.2944-0.11940.5089-0.0274-0.388-0.07430.13090.25140.2582-0.2612-0.3156-0.05762.4033-0.83960.63211.54080.11850.852847.28469.4488188.27
200.3806-0.2687-0.27450.22910.07770.640.3347-0.3776-0.05850.5341-0.21440.2345-0.2594-0.4279-0.30881.3818-0.52180.41060.9505-0.02050.779744.615275.5051154.0175
210.64010.35320.84541.0450.42871.69650.08450.06530.1818-0.24070.26070.44630.0002-0.5077-0.10261.0795-0.52210.06310.89080.060.981147.38863.7491116.5897
220.6537-0.4681-0.36610.46660.3060.2474-0.1489-0.01030.6561-0.30650.5183-0.4199-0.26360.37940.2780.8573-0.4174-0.26531.0017-0.06661.1428116.792482.6936119.8155
230.7694-0.48090.07020.9429-0.07510.92560.0498-0.2257-0.20690.5692-0.067-0.42510.70190.45190.1261.6914-0.5174-0.49311.10110.07361.1476108.425367.957151.7587
240.9132-0.40930.00790.1679-0.0061-0.0203-0.1105-0.1016-0.38670.20920.05330.0777-0.17440.08910.05351.0093-0.2483-0.15960.62520.23120.776382.40542.4938191.0219
250.3318-0.2986-0.22640.28090.34040.8372-0.0431-0.3368-0.47020.2799-0.0949-0.0190.8261-0.1156-0.32381.3165-0.54860.10990.68550.06660.97857.22143.5147125.9131
260.20240.0148-0.07030.8754-0.62672.70760.2016-0.2065-0.32640.5234-0.22490.5783-0.0276-0.7071-0.28461.0928-0.4660.15670.74950.04740.970850.05557.0655124.2055
271.67480.8272-0.20960.402-0.09650.0115-0.16740.1203-0.5238-0.1211-0.19120.38130.2561-0.094-1.3791.1299-1.01730.14530.82510.13711.002551.324544.1712121.259
280.3446-0.1678-0.06410.26940.0121.18320.0493-0.1943-0.04130.2157-0.171-0.20330.3830.36650.01151.2763-0.2303-0.04920.61160.14010.917278.23543.4903119.1825
291.768-0.48750.16040.52550.18460.56030.2578-0.8250.57140.4056-0.02510.1556-0.06810.0206-0.07811.1137-0.40690.1990.80960.04821.05150.248871.3267125.907
300.67750.0692-0.20480.7984-0.2180.18510.0826-0.1732-0.22640.49060.01960.12310.0849-0.27750.4221.6877-0.88020.32511.08350.18111.012746.532944.9727158.1881
310.1101-0.07710.01760.0618-0.03810.0496-0.2848-0.0108-0.2913-0.021-0.0045-0.0076-0.0693-0.1110.00032.5282-0.91870.64082.26850.00611.588232.882253.9318196.6137
320.02040.0045-0.02520.06530.01470.0319-0.0862-0.0856-0.18080.1556-0.20850.1416-0.0970.107-0.00012.3691-0.65440.27831.93870.34981.582339.640435.218193.2179
330.52450.25310.07920.18060.1680.2712-0.1169-0.69190.02570.20420.0595-0.37110.0098-0.09-0.02662.3423-0.67630.49681.93970.29551.410742.67445.5501191.1534
340.1859-0.10350.0530.09490.03780.02560.5387-0.1345-1.10330.6642-0.00620.96270.9964-0.99710.03141.6723-0.19840.09551.0298-0.00971.478555.953584.670291.5292
350.1606-0.0868-0.03790.45840.19430.12060.4497-0.28950.39320.4306-0.01540.7756-0.2504-1.03970.00011.6709-0.28980.49411.3875-0.10241.362838.880490.9807152.5543
362.609-0.27821.76060.0268-0.1821.1893-0.5388-0.24890.42550.5197-0.03950.1523-0.611-0.1311-0.23882.3663-0.66790.57321.7939-0.08731.214337.844684.75186.336
370.0198-0.01540.00380.0075-0.0011-0.0001-0.0052-0.2705-0.49090.1701-0.3214-0.5526-0.10210.41480.00012.2944-0.33220.03541.1119-0.21851.470468.6174112.6449130.7576
380.33420.07830.02430.07680.11190.15290.2355-0.2046-0.06930.4277-0.27410.4254-0.4616-0.2755-0.00021.7946-0.2810.30211.0922-0.1571.129153.7098104.8043141.9631
390.0138-0.0083-0.02040.00180.01010.0193-0.2137-0.3040.37790.06320.41620.1757-0.0326-0.28360.00022.3277-0.30630.2611.7612-0.27921.438744.3713101.8033166.7921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 215 )A1 - 215
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 264 )A216 - 264
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 446 )A265 - 446
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 223 )B15 - 223
5X-RAY DIFFRACTION5chain 'B' and (resid 224 through 293 )B224 - 293
6X-RAY DIFFRACTION6chain 'B' and (resid 294 through 439 )B294 - 439
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 32 )C2 - 32
8X-RAY DIFFRACTION8chain 'C' and (resid 33 through 286 or resid 1101 )C33 - 286
9X-RAY DIFFRACTION8chain 'C' and (resid 33 through 286 or resid 1101 )C1101
10X-RAY DIFFRACTION9chain 'C' and resid 1001C1001
11X-RAY DIFFRACTION10chain 'C' and resid 1002C1002
12X-RAY DIFFRACTION11chain 'C' and (resid 287 through 379 )C287 - 379
13X-RAY DIFFRACTION12chain 'D' and (resid 1 through 22 )D1 - 22
14X-RAY DIFFRACTION13chain 'D' and (resid 23 through 35 )D23 - 35
15X-RAY DIFFRACTION14chain 'D' and (resid 36 through 57 or resid 1001)D36 - 57
16X-RAY DIFFRACTION14chain 'D' and (resid 36 through 57 or resid 1001)D1001
17X-RAY DIFFRACTION15chain 'D' and (resid 58 through 84 )D58 - 84
18X-RAY DIFFRACTION16chain 'D' and (resid 85 through 131 )D85 - 131
19X-RAY DIFFRACTION17chain 'D' and (resid 132 through 151 )D132 - 151
20X-RAY DIFFRACTION18chain 'D' and (resid 152 through 178 )D152 - 178
21X-RAY DIFFRACTION19chain 'D' and (resid 179 through 197 )D179 - 197
22X-RAY DIFFRACTION20chain 'D' and (resid 198 through 231 )D198 - 231
23X-RAY DIFFRACTION21chain 'D' and (resid 232 through 241 )D232 - 241
24X-RAY DIFFRACTION22chain 'E' and (resid 1 through 15 )E1 - 15
25X-RAY DIFFRACTION23chain 'E' and (resid 16 through 73 )E16 - 73
26X-RAY DIFFRACTION24chain 'E' and (resid 74 through 196 or resid 1001)E74 - 196
27X-RAY DIFFRACTION24chain 'E' and (resid 74 through 196 or resid 1001)E1001
28X-RAY DIFFRACTION25chain 'F' and (resid 6 through 51 )F6 - 51
29X-RAY DIFFRACTION26chain 'F' and (resid 52 through 79 )F52 - 79
30X-RAY DIFFRACTION27chain 'F' and (resid 80 through 90 )F80 - 90
31X-RAY DIFFRACTION28chain 'F' and (resid 91 through 110 )F91 - 110
32X-RAY DIFFRACTION29chain 'G' and (resid 1 through 28 )G1 - 28
33X-RAY DIFFRACTION30chain 'G' and (resid 29 through 75 )G29 - 75
34X-RAY DIFFRACTION31chain 'H' and (resid 12 through 27 )H12 - 27
35X-RAY DIFFRACTION32chain 'H' and (resid 28 through 45 )H28 - 45
36X-RAY DIFFRACTION33chain 'H' and (resid 46 through 78 )H46 - 78
37X-RAY DIFFRACTION34chain 'I'I20 - 70
38X-RAY DIFFRACTION35chain 'J' and (resid 1 through 46 )J1 - 46
39X-RAY DIFFRACTION36chain 'J' and (resid 47 through 61 )J47 - 61
40X-RAY DIFFRACTION37chain 'K' and (resid 2 through 7 )K2 - 7
41X-RAY DIFFRACTION38chain 'K' and (resid 8 through 36 )K8 - 36
42X-RAY DIFFRACTION39chain 'K' and (resid 37 through 53 )K37 - 53

+
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