[English] 日本語
Yorodumi
- PDB-1ntk: Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ntk
TitleCrystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 7
  • Cytochrome b
  • UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL
  • Ubiquinol-cytochrome C reductase 8 kDa protein
  • cytochrome c1
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN
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 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 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 / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AY1 / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 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 ...Chem-AY1 / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 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 / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsGao, X. / Wen, X. / Esser, L. / Quinn, B. / Yu, L. / Yu, C.-A. / Xia, D.
CitationJournal: Biochemistry / Year: 2003
Title: Structural basis for the quinone reduction in the bc(1) complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc(1) with bound substrate and inhibitors at the Q(i) site
Authors: Gao, X. / Wen, X. / Esser, L. / Quinn, B. / Yu, L. / Yu, C.-A. / Xia, D.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 16, 2016Group: Non-polymer description
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Authors informed that for residue 22 of chain K, a GLN fits better in the density map than a SER. ...Authors informed that for residue 22 of chain K, a GLN fits better in the density map than a SER. They do not know if this represents a natural mutation or variant.

-
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
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, 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: Ubiquinol-cytochrome C reductase 8 kDa protein
J: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,75516
Polymers239,19511
Non-polymers2,5605
Water6,161342
1
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
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, 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: Ubiquinol-cytochrome C reductase 8 kDa protein
J: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules

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
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, 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: Ubiquinol-cytochrome C reductase 8 kDa protein
J: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,51032
Polymers478,39022
Non-polymers5,12010
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area99010 Å2
ΔGint-651 kcal/mol
Surface area165650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.785, 153.785, 592.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the two-fold axis: -x+1, -y+1, z.

-
Components

-
Ubiquinol-cytochrome C reductase complex ... , 7 types, 7 molecules ABFGHJK

#1: Protein Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial


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


Mass: 46575.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase
#6: Protein Ubiquinol-cytochrome C reductase complex 14 kDa protein / Complex III subunit VI


Mass: 13371.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00129, 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: 9606.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13271, 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: 9189.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00126, 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: 7209.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein Ubiquinol-cytochrome C reductase complex 6.4 kDa protein / Complex III subunit XI


Mass: 6568.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07552, quinol-cytochrome-c reductase

-
Protein , 4 types, 4 molecules CDEI

#3: Protein Cytochrome b


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


Mass: 27323.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00125
#5: Protein UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, MITOCHONDRIAL / Rieske iron-sulfur protein / RISP


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
#9: Protein Ubiquinol-cytochrome C reductase 8 kDa protein / Complex III subunit IX


Mass: 5824.802 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

-
Non-polymers , 4 types, 347 molecules

#12: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-AY1 / [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 2-methylpropanoate


Mass: 534.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N2O9
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2
Details: PEG 4000, ammonium acetate, potassium chloride, glycerol, DMG/SPC, MOPS, pH 7.2, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMMOPS1reservoirpH7.2
320 mMammonium acetate1reservoir
420 %(w/v)glycerol1reservoir
50.1 %decanoyl-N-methylglucamide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 109171 / Num. obs: 107555 / % possible obs: 98.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1
Reflection shellResolution: 2.6→2.667 Å / % possible all: 95.3
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.904 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27049 3224 3 %RANDOM
Rwork0.23307 ---
all0.23421 107555 --
obs0.23421 104312 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.172 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16605 0 171 342 17118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02117588
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.98223826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.54732097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.815152969
X-RAY DIFFRACTIONr_chiral_restr0.260.22608
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213047
X-RAY DIFFRACTIONr_nbd_refined0.2560.39158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.51196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.3101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.518
X-RAY DIFFRACTIONr_mcbond_it0.951.510504
X-RAY DIFFRACTIONr_mcangle_it1.769216889
X-RAY DIFFRACTIONr_scbond_it2.97737084
X-RAY DIFFRACTIONr_scangle_it4.8474.56935
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.489 239
Rwork0.464 7233
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)
10.8458-0.13170.39591.7077-0.94982.04720.08370.01850.079-0.11290.06420.70320.128-0.7454-0.1480.4539-0.1160.08050.5893-0.00690.813431.796887.120293.4967
20.2938-0.0987-0.06181.4644-0.20170.71490.0442-0.15070.15710.3573-0.03270.31-0.1783-0.3091-0.01140.5403-0.11630.1760.3233-0.020.498248.65293.3117115.0683
30.825-0.4367-0.22161.80420.122.37850.1061-0.02160.1474-0.036-0.00720.1655-0.3967-0.1217-0.09880.3688-0.11020.01110.03310.00530.337468.7124104.179392.1055
40.7826-0.5739-0.00512.70120.04241.69850.01840.0527-0.0686-0.17660.020.51930.084-0.2959-0.03840.3557-0.1079-0.07450.13240.01450.439357.102586.531373.9852
51.07660.28670.57910.7660.56622.73920.013-0.31930.11910.3785-0.0218-0.006-0.1714-0.14270.00880.9468-0.27190.10530.48780.02180.480263.910769.5154152.7401
62.4138-2.2514-0.81442.80121.9959-0.22260.3002-0.5489-0.72370.4354-0.31060.0544-0.37910.09630.01041.509-0.2229-0.07880.93940.21780.64281.038556.823172.6254
70.9941-0.11341.16761.1508-0.76044.83470.091-0.5354-0.0850.56610.011-0.159-0.0134-0.0559-0.10190.9326-0.32570.1040.52580.12090.559663.190245.9996152.7552
80000000000000000.6437000.643700.6437000
90.4939-0.46930.25850.22250.02354.3872-0.0408-0.42390.07580.42470.12930.0495-0.204-0.6887-0.08851.0943-0.28480.26840.75310.01390.575945.817872.0186159.9303
101.31250.55780.4743.43010.71962.19580.0222-0.4625-0.16070.92360.041-0.02860.1398-0.0617-0.06321.6288-0.23050.25531.44220.13450.693354.28367.2418193.1325
111.86210.16861.2911.03541.1143.80040.0509-0.52780.15510.4042-0.19510.289-0.1743-0.940.14410.9122-0.23480.3380.53140.00890.653843.123781.8561141.8616
123.9179-0.51671.078-0.8899-0.59214.3197-0.459-1.30630.33871.12590.2513-0.5187-0.62-0.65840.20772.8176-0.19020.08731.9579-0.37451.408773.3372112.8209188.7543
133.8014-0.9552-1.69551.4170.16211.8103-0.0607-0.2822-0.33890.24580.00590.20780.487-0.27130.05480.69-0.28790.06490.26190.03860.384258.787646.9683122.4786
140.55260.01160.08641.4922-1.10962.64490.035-0.5448-0.17440.54180.09960.2183-0.0525-0.4326-0.13460.8102-0.28590.18050.67340.11730.594848.269753.4649146.5655
157.2659-4.901-0.22837.1746.60313.2392-0.3944-0.6216-0.56020.95070.3070.81850.1633-0.18670.08741.9169-0.35580.4171.63210.60471.083736.726145.1569197.4681
16-0.50080.8010.3180.9632-1.58951.15490.411-0.09780.13730.0607-0.9631-0.49360.009-0.12780.55211.6134-0.40390.41691.46160.28031.054139.811650.4281186.4808
170000000000000000.6437000.643700.6437000
181.9403-0.088-1.13442.10370.9866-0.1885-0.0246-0.5498-0.02110.6475-0.00710.2588-0.0881-0.70950.03171.2163-0.17870.39031.0601-0.13220.81938.552389.0294161.2891
191.04851.0041-2.7044.066-5.871316.2680.3071-0.66590.19430.67050.00710.3763-0.8296-0.1977-0.31421.1164-0.11740.14040.6687-0.22940.704652.1423104.3129148.0676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2311 - 231
3X-RAY DIFFRACTION2AA232 - 446232 - 446
5X-RAY DIFFRACTION3BB17 - 23517 - 235
7X-RAY DIFFRACTION4BB236 - 439236 - 439
9X-RAY DIFFRACTION5CC2 - 1332 - 133
10X-RAY DIFFRACTION5CC173 - 264173 - 264
11X-RAY DIFFRACTION5CL - M381 - 3821
14X-RAY DIFFRACTION6CC134 - 172134 - 172
15X-RAY DIFFRACTION7CC265 - 379265 - 379
16X-RAY DIFFRACTION7CN3831
18X-RAY DIFFRACTION9DD173 - 241173 - 241
20X-RAY DIFFRACTION10DD1 - 1721 - 172
21X-RAY DIFFRACTION10DO2421
22X-RAY DIFFRACTION11EE1 - 711 - 71
24X-RAY DIFFRACTION12EE72 - 19672 - 196
25X-RAY DIFFRACTION13FF6 - 1106 - 110
27X-RAY DIFFRACTION14GG1 - 791 - 79
29X-RAY DIFFRACTION15HH3 - 523 - 52
30X-RAY DIFFRACTION16HH53 - 7853 - 78
32X-RAY DIFFRACTION17HH49 - 7849 - 78
33X-RAY DIFFRACTION18JJ2 - 612 - 61
35X-RAY DIFFRACTION19KK1 - 531 - 53
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.019
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.851
LS refinement shell
*PLUS
Rfactor Rfree: 0.49 / Rfactor Rwork: 0.47

+
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