[English] 日本語
Yorodumi
- PDB-3h1i: Stigmatellin and antimycin bound cytochrome bc1 complex from chicken -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h1i
TitleStigmatellin and antimycin bound cytochrome bc1 complex from chicken
Components
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • (UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ...) x 4
  • (UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ...) x 2
  • CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
  • Cytochrome b
KeywordsOXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEASE / UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / STIGMATELLIN / ANTIMYCIN / Electron transport / Heme / Iron / Membrane / Metal-binding / Mitochondrion / Mitochondrion inner membrane / Transmembrane / Transport / Disulfide bond / Iron-sulfur / Transit peptide
Function / homology
Function and homology information


Respiratory electron transport / Complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity ...Respiratory electron transport / Complex III assembly / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / heme binding / protein-containing complex / mitochondrion / metal ion binding / membrane / cytoplasm
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / 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 I / Cytochrome Bc1 Complex; Chain I / 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 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / 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 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 / 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. / 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 / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ANY / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DIUNDECYL PHOSPHATIDYL CHOLINE / STIGMATELLIN A / Unknown ligand / Cytochrome c ...Chem-ANY / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DIUNDECYL PHOSPHATIDYL CHOLINE / STIGMATELLIN A / Unknown ligand / Cytochrome c / Complex III subunit 9 / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsZhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H.
Citation
Journal: Nature / Year: 1998
Title: Electron Transfer by Domain Movement in Cytochrome Bc1
Authors: Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial Bc(1) Complex: A New Crystal Structure Reveals an Altered Intramolecular Hydrogen-Bonding Pattern.
Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
#2: Journal: J.BIOENERG.BIOMEMBR. / Year: 1999
Title: The Structure of the Avian Mitochondrial Cytochrome bc1 Complex.
Authors: Berry, E.A. / Huang, L.S. / Zhang, Z. / Kim, S.H.
History
DepositionApr 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Sep 6, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL
B: UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL
C: Cytochrome b
D: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN
G: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
H: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN
N: UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL
O: UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL
P: Cytochrome b
Q: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
R: Cytochrome b-c1 complex subunit Rieske, mitochondrial
S: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN
T: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
U: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN
V: Cytochrome b-c1 complex subunit Rieske, mitochondrial
W: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,02456
Polymers462,06520
Non-polymers17,95936
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area109030 Å2
ΔGint-716 kcal/mol
Surface area152830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.693, 181.666, 240.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO

#1: Protein UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I, MITOCHONDRIAL / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX31*PLUS, quinol-cytochrome-c reductase
#2: Protein UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2, MITOCHONDRIAL / COMPLEX III SUBUNIT II


Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX29*PLUS, quinol-cytochrome-c reductase

-
Protein , 2 types, 4 molecules CPDQ

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


Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946, quinol-cytochrome-c reductase
#4: Protein CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL / CYTOCHROME C-1


Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX26*PLUS, quinol-cytochrome-c reductase

-
Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules ERIV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex ...Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex III subunit 5


Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: sequence database residues 77-272 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex ...Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP / Complex III subunit 5


Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-76 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase

-
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ... , 4 types, 8 molecules FSGTHUJW

#6: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KDA PROTEIN / COMPLEX III SUBUNIT VI


Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX30*PLUS, quinol-cytochrome-c reductase
#7: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C / UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 9.5 KDA PROTEIN / COMPLEX III SUBUNIT VII


Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: quinol-cytochrome-c reductase
#8: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 11 KDA PROTEIN / MITOCHONDRIAL HINGE PROTEIN / CYTOCHROME C1 / NONHEME 11 KDA PROTEIN / COMPLEX III SUBUNIT VIII


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: quinol-cytochrome-c reductase
#10: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.2 KDA PROTEIN / CYTOCHROME C1 / NONHEME 7 KDA PROTEIN / COMPLEX III SUBUNIT X


Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: D0VX27*PLUS, quinol-cytochrome-c reductase

-
Non-polymers , 10 types, 36 molecules

#11: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#12: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#13: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#14: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42O7
#15: Chemical ChemComp-ANY / 2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2-HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL-4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER / ANTIMYCIN


Mass: 562.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H42N2O9
#16: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#17: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#18: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#20: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM

-
Details

Sequence detailsIN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ...IN THE COORDINATES THE FIRST 15 RESIDUES IN CHAINS I AND V ARE MODELED AS UNK BECAUSE THE SEQUENCE ALIGNMENT IS UNKNOWN FOR THE FIRST 42 RESIDUES IN CHAINS I AND V.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 20MM KMES PH 6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000, INHIBITORS WERE ADDED FROM ETHANOLIC SOLUTION, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 29, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54121
21.54181
ReflectionResolution: 3.5→87.039 Å / Num. all: 90316 / Num. obs: 90316 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 73.1 Å2 / Rsym value: 0.229 / Net I/σ(I): 7.01
Reflection shellResolution: 3.5→3.63 Å / Mean I/σ(I) obs: 1.34 / Rsym value: 0.997 / % possible all: 91.3

-
Processing

Software
NameVersionClassification
ALMNmodel building
TFFC(CCP4 PACKAGE)model building
RAVEmodel building
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
ALMNphasing
TFFC(CCP4 PACKAGE)phasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BCC

1bcc


Resolution: 3.53→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6933881.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2551 3 %RANDOM
Rwork0.263 ---
all0.264 85111 --
obs0.264 85111 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.3956 Å2 / ksol: 0.230235 e/Å3
Displacement parametersBiso mean: 89.2 Å2
Baniso -1Baniso -2Baniso -3
1-34.71 Å20 Å20 Å2
2---20.96 Å20 Å2
3----13.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.53→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31797 0 904 0 32701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.452.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.53→3.71 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.406 351 3.2 %
Rwork0.381 10734 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2hetero10.par&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3fnmfmx.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5prosthw.par&_1_TOPOLOGY_INFILE_5

+
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