[English] 日本語
Yorodumi
- PDB-1bgy: CYTOCHROME BC1 COMPLEX FROM BOVINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bgy
TitleCYTOCHROME BC1 COMPLEX FROM BOVINE
Components(CYTOCHROME BC1 ...) x 11
KeywordsELECTRON TRANSPORT / CYTOCHROME / MEMBRANE PROTEIN
Function / homology
Function and homology information


Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-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 / metal ion binding / membrane
Similarity search - Function
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 ...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 / 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 8 superfamily / 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 b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / 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 ...FE2/S2 (INORGANIC) CLUSTER / HEME C / 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 / molecular replacement / Resolution: 3 Å
AuthorsIwata, S. / Lee, J.W. / Okada, K. / Lee, J.K. / Iwata, M. / Ramaswamy, S. / Jap, B.K.
CitationJournal: Science / Year: 1998
Title: Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex.
Authors: Iwata, S. / Lee, J.W. / Okada, K. / Lee, J.K. / Iwata, M. / Rasmussen, B. / Link, T.A. / Ramaswamy, S. / Jap, B.K.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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_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.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
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME BC1 COMPLEX
B: CYTOCHROME BC1 COMPLEX
C: CYTOCHROME BC1 COMPLEX
D: CYTOCHROME BC1 COMPLEX
E: CYTOCHROME BC1 COMPLEX
F: CYTOCHROME BC1 COMPLEX
G: CYTOCHROME BC1 COMPLEX
H: CYTOCHROME BC1 COMPLEX
I: CYTOCHROME BC1 COMPLEX
J: CYTOCHROME BC1 COMPLEX
K: CYTOCHROME BC1 COMPLEX
M: CYTOCHROME BC1 COMPLEX
N: CYTOCHROME BC1 COMPLEX
O: CYTOCHROME BC1 COMPLEX
P: CYTOCHROME BC1 COMPLEX
Q: CYTOCHROME BC1 COMPLEX
R: CYTOCHROME BC1 COMPLEX
S: CYTOCHROME BC1 COMPLEX
T: CYTOCHROME BC1 COMPLEX
U: CYTOCHROME BC1 COMPLEX
V: CYTOCHROME BC1 COMPLEX
W: CYTOCHROME BC1 COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,15129
Polymers482,27222
Non-polymers3,8797
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area83890 Å2
ΔGint-581 kcal/mol
Surface area166000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.110, 130.110, 720.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.066, 0.136, 0.988), (0.136, -0.98, 0.144), (0.988, 0.144, 0.046)
Vector: 1.325, 184.252, -26.658)

-
Components

-
CYTOCHROME BC1 ... , 11 types, 22 molecules AMBNCODPEQFRGSHTIUJVKW

#1: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P23004, quinol-cytochrome-c reductase
#3: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00157, quinol-cytochrome-c reductase
#4: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00125, quinol-cytochrome-c reductase
#5: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 13371.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00129, quinol-cytochrome-c reductase
#7: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13271, quinol-cytochrome-c reductase
#8: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00126, quinol-cytochrome-c reductase
#9: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7964.259 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein CYTOCHROME BC1 COMPLEX / UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / COMPLEX III


Mass: 6370.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MITOCHONDRIAL INNER MEMBRANE / Organ: HEART / Organelle: MITOCHONDRION / Tissue: HEART MUSCLE / References: UniProt: P07552, quinol-cytochrome-c reductase

-
Non-polymers , 3 types, 7 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-HEC / HEME C


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


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 61.5 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.015 %n-dodecyl-beta-D-maltoside11
2100 mM11NaCl
38 %PEG400011
4HECAMEG11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 111672 / % possible obs: 81.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.92 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.9 / % possible all: 27.9
Reflection
*PLUS
Num. measured all: 440419
Reflection shell
*PLUS
% possible obs: 27.9 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1BE3

1be3


Resolution: 3→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.36 2022 2 %RANDOM
Rwork0.32 ---
obs-101111 74 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31468 0 262 0 31730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.7363
X-RAY DIFFRACTIONp_mcangle_it2.683.5
X-RAY DIFFRACTIONp_scbond_it3.0334
X-RAY DIFFRACTIONp_scangle_it4.4375.5
X-RAY DIFFRACTIONp_plane_restr0.02490.03
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.2220.3
X-RAY DIFFRACTIONp_multtor_nbd0.30.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2330.3
X-RAY DIFFRACTIONp_planar_tor6.27
X-RAY DIFFRACTIONp_staggered_tor26.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.420
X-RAY DIFFRACTIONp_special_tor

+
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