[English] 日本語
Yorodumi
- PDB-2fyu: Crystal structure of bovine heart mitochondrial bc1 with jg144 in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fyu
TitleCrystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor
Components
  • (Ubiquinol-cytochrome c reductase complex ...) x 4
  • (Ubiquinol-cytochrome c reductase iron-sulfur subunit, ...) x 2
  • (Ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Hypothetical protein LOC616871
KeywordsOXIDOREDUCTASE / Transmembrane helices / 11 protein complex
Function / homology
Function and homology information


Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / : / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma 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 / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / 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 c1, transmembrane anchor, C-terminal / 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 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / 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. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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] iron-sulphur domain / Rieske [2Fe-2S] 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-FDN / 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-FDN / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsXia, D. / Esser, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc1 complex.
Authors: Esser, L. / Gong, X. / Yang, S. / Yu, L. / Yu, C.A. / Xia, D.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_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.ptnr2_label_atom_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_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: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial
F: Hypothetical protein LOC616871
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 iron-sulfur subunit, mitochondrial
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)243,63716
Polymers241,29311
Non-polymers2,3445
Water4,810267
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, mitochondrial
F: Hypothetical protein LOC616871
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 iron-sulfur subunit, mitochondrial
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, mitochondrial
F: Hypothetical protein LOC616871
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 iron-sulfur subunit, mitochondrial
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)487,27432
Polymers482,58722
Non-polymers4,68710
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area101970 Å2
ΔGint-676 kcal/mol
Surface area163640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.263, 154.263, 590.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe second part of the biological assembly (dimer) is generated by the two fold rotation axis: 1-x,1-y, z.

-
Components

-
Ubiquinol-cytochrome-c reductase complex core protein ... , 2 types, 2 molecules AB

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


Mass: 49266.254 Da / Num. of mol.: 1 / Fragment: Core1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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 / Fragment: Core2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase

-
Protein , 3 types, 3 molecules CDF

#3: Protein Cytochrome b


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


Mass: 27323.277 Da / Num. of mol.: 1 / Fragment: cytochrome c1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125
#6: Protein Hypothetical protein LOC616871


Mass: 13371.190 Da / Num. of mol.: 1 / Fragment: subunit 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129

-
Ubiquinol-cytochrome c reductase iron-sulfur subunit, ... , 2 types, 2 molecules EI

#5: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial / RISP


Mass: 21640.580 Da / Num. of mol.: 1 / Fragment: Iron-sulfur protein / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#9: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial


Mass: 7964.259 Da / Num. of mol.: 1 / Fragment: Iron-sulfur protein signal sequence / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272

-
Ubiquinol-cytochrome c reductase complex ... , 4 types, 4 molecules GHJK

#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 / Fragment: subunit 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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 / Fragment: subunit 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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 / Fragment: subunit 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein Ubiquinol-cytochrome c reductase complex 6.4 kDa protein / Complex III subunit XI


Mass: 6527.604 Da / Num. of mol.: 1 / Fragment: subunit 11 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07552, quinol-cytochrome-c reductase

-
Non-polymers , 4 types, 272 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-FDN / (5S)-3-ANILINO-5-(2,4-DIFLUOROPHENYL)-5-METHYL-1,3-OXAZOLIDINE-2,4-DIONE / 5-(2,4-DIFLUORO-PHENYL)-5-METHYL-3-PHENYLAMINO-OXAZOLIDINE-2,4-DIONE


Mass: 318.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12F2N2O3
#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.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM MOPS 7.2pH, 20 mM Ammonium acetate, 20% glycerol.Incubation with 2-5 mol excess of JG144. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57, VAPOR DIFFUSION, ...Details: 50 mM MOPS 7.2pH, 20 mM Ammonium acetate, 20% glycerol.Incubation with 2-5 mol excess of JG144. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.009 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 3, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 157290 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.3 / Redundancy: 4 % / Rsym value: 0.056 / Net I/σ(I): 17.2
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.382 / Num. unique all: 13582 / % possible all: 42.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1l0n

1l0n


Resolution: 2.26→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.1 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28328 3230 2 %RANDOM
Rwork0.24843 ---
all0.24916 157290 --
obs0.24916 157290 96.89 %-
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: 25.239 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2--2.36 Å20 Å2
3----4.71 Å2
Refinement stepCycle: LAST / Resolution: 2.26→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16477 0 156 267 16900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02117444
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.98323647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.115102088
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_restr0.20.22575
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.0213008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1170.27426
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.2193
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5920.410459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5143.80116826
X-RAY DIFFRACTIONr_scbond_it5.68636985
X-RAY DIFFRACTIONr_scangle_it7.3144.56819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 200
Rwork0.316 10142
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)
10.6387-0.0310.38091.1171-0.9111.93340.10770.02880.0087-0.19850.0510.48240.0513-0.6601-0.15870.409-0.1203-0.02160.51920.00040.648431.848587.378192.8341
20.40190.04650.05191.2591-0.27081.21260.0627-0.10140.1320.0991-0.05440.1683-0.1467-0.3382-0.00830.3791-0.13150.07820.2501-0.0220.429948.955493.6085114.8425
30.7853-0.47420.04761.68350.22322.16170.08850.03660.1677-0.1045-0.06210.0211-0.257-0.1692-0.02640.3716-0.10620.01210.03050.00410.380468.9613104.585991.8809
40.9661-0.5856-0.00492.51750.01181.40070.03560.057-0.0577-0.18780.00940.32910.1252-0.1548-0.04490.4149-0.0943-0.07230.12530.00660.386557.164186.605373.2507
50.67740.15260.2280.36060.57391.06570.0555-0.23010.04180.1964-0.02140.0307-0.0985-0.0703-0.03410.5667-0.29450.04320.30590.02340.408364.906868.7511154.1684
61.8003-0.78590.00812.81950.55981.7729-0.03-0.1901-0.06520.35760.0574-0.25210.15070.2677-0.02740.7502-0.3258-0.07880.49330.10510.422481.270957.0226172.1093
71.21750.13270.40991.06840.26073.00460.1008-0.3079-0.18690.2534-0.0423-0.04360.41710.0118-0.05850.5908-0.30950.00580.27410.11520.505364.794544.9222152.9122
80000000000000000.52000.5200.52000
90.5907-0.1591-0.6957-0.1286-0.08287.78640.0257-0.2403-0.0080.2387-0.09270.15730.2128-0.60550.0670.6332-0.34220.14870.50520.03240.491345.351371.5948159.1567
101.84740.35720.29362.54280.17841.34420.0143-0.5153-0.13530.63180.00970.04380.0101-0.1603-0.0240.981-0.31050.16610.91810.08510.430654.585867.6302192.8498
111.23560.3402-1.15970.5191-0.38352.96050.0755-0.3259-0.0270.1692-0.087-0.17510.03460.65960.01160.4672-0.2006-0.16130.424-0.00440.5649110.936172.0527141.5949
124.8487-1.63980.43475.0189-0.22114.4109-0.3117-1.1715-0.12150.83050.5055-0.13550.35010.6179-0.19391.0334-0.0993-0.02050.9830.25110.575282.338742.078188.3545
133.0455-0.9906-1.26721.19160.00511.75740.0234-0.0737-0.29960.0907-0.06650.20120.4608-0.17690.04310.5112-0.30320.01370.19760.02240.424459.045347.1643122.0445
140.3252-0.0878-0.14471.42-1.5012.26130.0528-0.2983-0.07940.41690.05240.1455-0.0529-0.3633-0.10520.5626-0.34880.07540.44550.04280.497448.046154.8256144.5844
153.6388-5.8928-1.095116.0242-3.53815.61790.0331-0.2262-0.76020.0920.00510.88150.4103-0.134-0.03820.7231-0.24930.08860.72740.09040.857940.081539.2536193.3643
165.5433-7.7302-3.484124.966-5.16082.8251-0.27790.2280.40050.38620.0625-0.26680.2818-0.65140.21540.7106-0.26220.05170.73640.07520.610939.858350.2342187.5459
170000000000000000.52000.5200.52000
181.38661.99983.50310.26.6415.59020.13930.5135-0.1719-0.4218-0.41410.47980.4614-1.9490.27480.53-0.0241-0.00950.5219-0.08130.692660.473994.92288.45
1918.47134.40517.76658.8431-5.157926.5690.8166-0.06050.2125-0.1709-0.03520.02570.7781-0.1364-0.78140.52560.02380.06340.59620.01050.811854.526280.928293.656
2083.762715.513-6.435449.178312.994326.3317-1.06531.9731-1.5905-0.29761.06841.4086-0.4297-0.044-0.00310.5201-0.0004-0.00220.5206-0.00280.521147.063598.0961104.0711
211.13420.0579-0.07022.2396-2.2327.4889-0.0997-0.42640.03580.38490.06060.1708-0.5538-0.95830.03910.6615-0.11830.22570.7295-0.10570.605738.913789.4213161.1124
221.94551.2355-2.41853.9323-4.031810.70330.2282-0.46930.25150.39230.06920.1913-0.5432-0.3154-0.29730.6605-0.08640.04780.5104-0.16290.609952.5445104.6869147.9947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2311 - 231
2X-RAY DIFFRACTION2AA232 - 446232 - 446
3X-RAY DIFFRACTION3BB17 - 23517 - 235
4X-RAY DIFFRACTION4BB236 - 439236 - 439
5X-RAY DIFFRACTION5CC3 - 1333 - 133
6X-RAY DIFFRACTION5CC173 - 264173 - 264
7X-RAY DIFFRACTION5CL381
8X-RAY DIFFRACTION6CC134 - 172134 - 172
9X-RAY DIFFRACTION7CC265 - 379265 - 379
10X-RAY DIFFRACTION8CM382
11X-RAY DIFFRACTION9DD173 - 241173 - 241
12X-RAY DIFFRACTION10DD1 - 1721 - 172
13X-RAY DIFFRACTION10DO242
14X-RAY DIFFRACTION11EE1 - 711 - 71
15X-RAY DIFFRACTION12EE72 - 19672 - 196
16X-RAY DIFFRACTION13FF6 - 1106 - 110
17X-RAY DIFFRACTION14GG1 - 751 - 75
18X-RAY DIFFRACTION15HH15 - 5215 - 52
19X-RAY DIFFRACTION16HH53 - 7853 - 78
20X-RAY DIFFRACTION17HH49 - 7849 - 78
21X-RAY DIFFRACTION18II2 - 262 - 26
22X-RAY DIFFRACTION19II27 - 5127 - 51
23X-RAY DIFFRACTION20II52 - 5752 - 57
24X-RAY DIFFRACTION21JJ2 - 612 - 61
25X-RAY DIFFRACTION22KK1 - 531 - 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://pdbjlvh1.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