[English] 日本語
Yorodumi
- PDB-1sqb: Crystal Structure Analysis of Bovine Bc1 with Azoxystrobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sqb
TitleCrystal Structure Analysis of Bovine Bc1 with Azoxystrobin
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 7
  • (Ubiquinol-cytochrome c reductase ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / cytochrome bc1 / Qo inhibitor / membrane protein / electron transport
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-AZO / 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-AZO / 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: 2.69 Å
AuthorsEsser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex
Authors: Esser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
#1: Journal: Science / Year: 1997
Title: Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria
Authors: Xia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A.M. / Zhang, L. / Yu, L. / Deisenhofer, J.
#2: Journal: Biochemistry / Year: 2002
Title: The crystal structure of mitochondrial cytochrome bc1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition.
Authors: Gao, X. / Wen, X. / Yu, C. / Esser, L. / Tsao, S. / Quinn, B. / Zhang, L. / Yu, L. / Xia, D.
History
DepositionMar 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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: Ubiquinol-cytochrome c reductase iron-sulfur subunit
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)248,82216
Polymers246,39311
Non-polymers2,4295
Water4,216234
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, heme protein, mitochondrial
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit
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, heme protein, mitochondrial
E: Ubiquinol-cytochrome c reductase iron-sulfur subunit
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)497,64432
Polymers492,78722
Non-polymers4,85710
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area102230 Å2
ΔGint-682 kcal/mol
Surface area164080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.554, 153.554, 596.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

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

#1: Protein Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial / Complex III subunit I


Mass: 52796.410 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: 48203.434 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 / 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 / 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 / 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: 6469.522 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 , 2 types, 2 molecules CD

#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, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein, mitochondrial / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00125, quinol-cytochrome-c reductase

-
Ubiquinol-cytochrome c reductase ... , 2 types, 2 molecules EI

#5: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit / Complex III subunit IX


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: 7964.259 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, 239 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-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
#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.: 234 / 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: 4 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 277 K / pH: 7.2
Details: 20mM ammonium acetate, 20% glycerol, 12% PEG4000, 0.5M KCl, 0.1% diheptanoyl-phosphatidylcholine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.91889
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2002 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91889 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 99537 / Observed criterion σ(I): 1
Reflection shellResolution: 2.69→2.72 Å / % possible all: 86.3

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1QCR

1qcr


Resolution: 2.69→40 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.863 / SU B: 18.314 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2866 3 %RANDOM
Rwork0.241 ---
obs0.242 91856 95.6 %-
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: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2--1.75 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.69→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16500 0 163 234 16897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02117529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.98723756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16952092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.22581
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1430.28189
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5391.510483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.014216864
X-RAY DIFFRACTIONr_scbond_it1.57637040
X-RAY DIFFRACTIONr_scangle_it2.6324.56878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 179
Rwork0.345 6379
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)
10.9050.07040.35151.005-0.71841.67360.10330.02660.0165-0.13260.01530.58930.0924-0.6479-0.11860.4452-0.10650.01770.496-0.02140.678231.608587.046693.8203
2-0.002-0.10440.24971.40450.06610.72780.093-0.12150.18910.1784-0.06730.226-0.1694-0.3524-0.02560.4259-0.15190.13510.2767-0.00630.434948.66793.2988115.7197
31.3547-0.3485-0.10181.49190.0012.12260.12470.05240.2446-0.0835-0.04410.0692-0.2945-0.1089-0.08060.3395-0.10520.00680.03270.00320.276468.6565104.209792.7738
41.0143-0.9101-0.20622.32750.01741.56620.05820.0258-0.0674-0.2049-0.05630.39950.0589-0.2101-0.00190.3656-0.0719-0.0840.1471-0.01060.366256.870686.195474.2242
50.67430.02340.37320.13770.76992.14220.0999-0.27560.09940.3684-0.11180.066-0.1119-0.27610.01190.7698-0.36830.08230.41810.02570.404262.349969.3126153.3841
60.7318-2.3630.1160.9458-0.54361.03090.1502-0.3451-0.27950.4047-0.0815-0.2370.33430.2041-0.06860.9997-0.4625-0.12110.70620.10590.607380.843356.4964173.2031
70.9732-0.2688-0.13440.95170.10391.6920.1402-0.3984-0.12010.3495-0.0826-0.10390.20330.1528-0.05760.7181-0.42880.02410.41250.11380.500663.887346.9273154.3152
80.7133-0.1773-1.17560.3484-0.89713.32790.0313-0.30310.07750.4368-0.07370.1970.0475-0.59590.04240.7931-0.40290.20450.56430.01450.470244.983871.4543159.8832
91.50220.32120.04731.62820.26680.8118-0.0366-0.5673-0.09960.63120.0961-0.03580.1143-0.1226-0.05951.3333-0.39960.20661.12720.05070.570354.132567.725193.6572
100.84380.13751.62380.67460.5595.70950.0415-0.23790.06090.2832-0.05530.2546-0.2852-0.42670.01370.571-0.30760.24020.4852-0.03180.568343.046881.9793142.432
116.80761.179-0.57398.2690.2077.8649-0.0183-0.00290.67750.59980.18580.040.1246-0.1866-0.16751.366-0.05080.05221.3135-0.14851.256270.7051111.2268190.0314
123.2002-1.137-1.0861.0927-0.02771.4857-0.0273-0.248-0.40240.22940.00070.21880.4057-0.1870.02650.5491-0.31970.00840.23580.02460.36358.632446.8265123.1983
130.3331-0.16290.06511.2625-1.81643.04540.0533-0.433-0.06470.34890.10010.12860.109-0.4714-0.15340.7423-0.36310.09740.48930.00360.539147.801554.5874145.5718
144.8971-5.7912-2.805411.04941.99186.64130.1951-0.4943-0.4575-0.25980.00640.23080.318-0.5099-0.20150.8563-0.4090.05490.95340.17270.89939.069640.727194.879
157.5042-11.3285-3.283723.6995-3.11336.02960.0843-0.03430.0965-0.0137-0.229-0.57980.4533-0.53790.14470.8461-0.33760.01450.91520.01940.726839.554950.1196188.3869
161.58891.0974.49967.86943.54936.39210.1880.561-0.4414-0.20120.02360.89730.539-0.3837-0.21150.6261-0.05820.09840.6026-0.13710.840158.432592.013588.0894
170.6408-0.0781-0.29011.7467-0.59672.07860.0888-0.41880.15440.49890.11180.3575-0.2287-0.6543-0.20060.8878-0.21670.27070.9017-0.09260.644838.397988.8394161.2071
180.89591.0384-1.48832.4006-3.218210.5260.0114-0.30330.06530.3049-0.01720.0981-0.3047-0.74290.00590.8074-0.11730.11690.61-0.20490.622251.781104.319148.7156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 23135 - 265
2X-RAY DIFFRACTION2AA232 - 446266 - 480
3X-RAY DIFFRACTION3BB17 - 23531 - 249
4X-RAY DIFFRACTION4BB236 - 439250 - 453
5X-RAY DIFFRACTION5CC2 - 1332 - 133
6X-RAY DIFFRACTION5CC173 - 264173 - 264
7X-RAY DIFFRACTION6CC134 - 172134 - 172
8X-RAY DIFFRACTION7CC265 - 379265 - 379
9X-RAY DIFFRACTION8DD173 - 241173 - 241
10X-RAY DIFFRACTION9DD1 - 1721 - 172
11X-RAY DIFFRACTION10EE1 - 711 - 71
12X-RAY DIFFRACTION11EE72 - 19672 - 196
13X-RAY DIFFRACTION12FF6 - 1106 - 110
14X-RAY DIFFRACTION13GG1 - 751 - 75
15X-RAY DIFFRACTION14HH12 - 5212 - 52
16X-RAY DIFFRACTION15HH53 - 7853 - 78
17X-RAY DIFFRACTION16II1 - 321 - 32
18X-RAY DIFFRACTION17JJ1 - 611 - 61
19X-RAY DIFFRACTION18KK2 - 532 - 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