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- PDB-1ezv: STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WIT... -

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Entry
Database: PDB / ID: 1ezv
TitleSTRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT
Components
  • (UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ...) x 6
  • CYTOCHROME B
  • CYTOCHROME C1
  • HEAVY CHAIN (VH) OF FV-FRAGMENT
  • LIGHT CHAIN (VL) OF FV-FRAGMENT
  • UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / cytochrome bc1 complex / complex III / QCR / mitochondria / yeast / antibody Fv-fragment / stigmatellin / coenzyme Q6 / matrix processing peptidases / ubiquinone / electron transfer / proton transfer / Q-cycle / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade ...Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / matrix side of mitochondrial inner membrane / FCERI mediated Ca+2 mobilization / protein processing involved in protein targeting to mitochondrion / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Respiratory electron transport / Regulation of actin dynamics for phagocytic cup formation / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / immunoglobulin complex / mitochondrial crista / immunoglobulin mediated immune response / aerobic respiration / antigen binding / proton transmembrane transport / nuclear periphery / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / adaptive immune response / oxidoreductase activity / immune response / heme binding / mitochondrion / proteolysis / extracellular space / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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 c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 ...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 c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 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 / 3-layer Sandwich / 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] 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Helix Hairpins / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / STIGMATELLIN A / Chem-UQ6 / : / : / : / : / : / : ...FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / STIGMATELLIN A / Chem-UQ6 / : / : / : / : / : / : / : / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Ig kappa chain V-V region HP 124E1 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Ig heavy chain V region 3-6 / Cytochrome b-c1 complex subunit 9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsHunte, C. / Koepke, J. / Lange, C. / Rossmanith, T. / Michel, H.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure at 2.3 A resolution of the cytochrome bc(1) complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment.
Authors: Hunte, C. / Koepke, J. / Lange, C. / Rossmanith, T. / Michel, H.
History
DepositionMay 12, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
B: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B
D: CYTOCHROME C1
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
H: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
F: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
G: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
I: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
X: HEAVY CHAIN (VH) OF FV-FRAGMENT
Y: LIGHT CHAIN (VL) OF FV-FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,12417
Polymers243,99111
Non-polymers3,1336
Water6,233346
1
A: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
B: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B
D: CYTOCHROME C1
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
H: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
F: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
G: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
I: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
hetero molecules

A: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I
B: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B
D: CYTOCHROME C1
E: UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
H: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN
F: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN
G: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C
I: UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN
X: HEAVY CHAIN (VH) OF FV-FRAGMENT
Y: LIGHT CHAIN (VL) OF FV-FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,95632
Polymers461,69120
Non-polymers6,26612
Water36020
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y,-z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.47, 163.92, 147.27
Angle α, β, γ (deg.)90, 117.50, 90
Int Tables number5
Space group name H-MC121
DetailsThe yeast mitochondrial cytochrome bc1 complex consist of 9 subunits (COR1, QCR2, COB, CYT1, RIP1, QCR6, QCR7, QCR8, QCR9). The biological functional unit is a homodimer. The smallest subunit QCR10, which is not required for a functional enzyme, was not present in the protein preparations. / The cytochrome bc1 complex was co-crystallized with an antibody Fv-fragment, which is bound to subunit RIP1 ("Rieske"-protein). The Fv-fragment consists of heavy and light chain (VH and VL). the Fv-fragment is bound to the "Rieske"-protein (chain ID E)

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Components

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UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX ... , 6 types, 6 molecules ABHFGI

#1: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I


Mass: 47358.168 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: MITOCHONDRIA, YEAST, SACCHAROMYCES CEREVISIAE / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07256, quinol-cytochrome-c reductase
#2: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 38751.918 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: FV-FRAGMENT DERIVED FROM THE MURINE MONOCLONAL ANTIBODY 18E11, EXPRESSION SYSTEM ESCHERICHIA COLI
Organelle: MITOCHONDRIAMitochondrion
References: GenBank: 786302, UniProt: P07257*PLUS, quinol-cytochrome-c reductase
#6: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN


Mass: 8854.792 Da / Num. of mol.: 1 / Fragment: RESIDUES 74-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion
References: GenBank: 836788, UniProt: P00127*PLUS, quinol-cytochrome-c reductase
#7: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN


Mass: 14355.443 Da / Num. of mol.: 1 / Fragment: RESIDUES 3-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion
References: GenBank: 927796, UniProt: P00128*PLUS, quinol-cytochrome-c reductase
#8: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C


Mass: 10856.314 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion
References: GenBank: 1008356, UniProt: P08525*PLUS, quinol-cytochrome-c reductase
#9: Protein UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN


Mass: 6301.232 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P22289, quinol-cytochrome-c reductase

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Protein , 3 types, 3 molecules CDE

#3: Protein CYTOCHROME B /


Mass: 43674.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: GenBank: 643021, UniProt: P00163*PLUS
#4: Protein CYTOCHROME C1 /


Mass: 27423.904 Da / Num. of mol.: 1 / Fragment: RESIDUES 62-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion / References: GenBank: 1420211, UniProt: P07143*PLUS
#5: Protein UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT


Mass: 20122.955 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organelle: MITOCHONDRIAMitochondrion
References: GenBank: 602391, UniProt: P08067*PLUS, quinol-cytochrome-c reductase

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Antibody , 2 types, 2 molecules XY

#10: Antibody HEAVY CHAIN (VH) OF FV-FRAGMENT


Mass: 14365.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P18531*PLUS
#11: Antibody LIGHT CHAIN (VL) OF FV-FRAGMENT


Mass: 11926.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01647*PLUS

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Non-polymers , 5 types, 352 molecules

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


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O7
#14: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H60O4
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 73.85 %
Crystal growTemperature: 277 K / Method: microseeding / pH: 8
Details: 5 % PEG 4000, 100 mM Tris, 0.05 % Undecyl-maltoside, 1 micromolar stigmatellin, pH 8.0, microseeding, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
3100 mMTris-HCl1drop
40.05 %UDM1drop
55-6 %PEG40001reservoir
1protein1drop
2PEG40001drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
22771
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-310.931
SYNCHROTRONEMBL/DESY, Hamburg X1120.906
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 1, 1999
MAR scanner 345 mm plate2IMAGE PLATEMay 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
20.9061
ReflectionResolution: 2.3→15 Å / Num. all: 168625 / % possible obs: 84.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 6.27 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→15 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.39 / Num. unique all: 4845 / % possible all: 73.9
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 168625 / Num. measured all: 1057968
Reflection shell
*PLUS
% possible obs: 73.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
ARP/wARPmodel building
CNSrefinement
DMphasing
RefinementResolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4240 -RANDOM
Rwork0.222 ---
all0.223 199009 --
obs0.253 168517 84.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17222 0 213 346 17781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_torsion_deg24.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 2.5 % / Rfactor all: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 0.9

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