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- EMDB-1876: Structural basis of substrate shuttling in bovine mitochondrial s... -

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Entry
Database: EMDB / ID: EMD-1876
TitleStructural basis of substrate shuttling in bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM
Map data3D cryo-EM map of supercomplex B (I1III2IV1) from bovine heart mitochondria
Sample
  • Sample: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria
  • Protein or peptide: NADH-dehydrogenaseNADH dehydrogenase
  • Protein or peptide: Cytochrome c reductase
  • Protein or peptide: Cytochrome c oxidase
  • Protein or peptide: Cytochrome c
KeywordsSupercomplex B / mitochondria / respiratory chain / complex I / complex III / complex IV / amphipol A8-35 / random conical tilt
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex IV / NADH dehydrogenase (quinone) activity / mitochondrial respiratory chain complex III assembly / regulation of oxidative phosphorylation / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / respiratory chain complex I / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / molybdopterin cofactor binding / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / iron-sulfur cluster assembly / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / respirasome / respiratory electron transport chain / ferric iron binding / central nervous system development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / iron ion binding / copper ion binding / apoptotic process / heme binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Frataxin/CyaY superfamily / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII ...NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Frataxin/CyaY superfamily / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / : / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / 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 c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome c oxidase subunit III / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Molybdopterin dinucleotide-binding domain / Cytochrome c oxidase subunit III-like superfamily / Molydopterin dinucleotide binding 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 C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c, class IA/ IB / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / 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 / Copper centre Cu(A) / Cytochrome C oxidase subunit II, transmembrane domain superfamily / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site
Similarity search - Domain/homology
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 c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial ...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 c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / 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 / Cytochrome c / Cytochrome c oxidase subunit 2 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 15
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsAlthoff T / Mills DJ / Popot J-L / Kuehlbrandt W
Citation
Journal: EMBO J / Year: 2011
Title: Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1.
Authors: Thorsten Althoff / Deryck J Mills / Jean-Luc Popot / Werner Kühlbrandt /
Abstract: The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. ...The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred.
#1: Year: 2011
Title: Strukturelle Untersuchungen am Superkomplex I1III2IV1 der Atmungskette mittels Kryoelektronenmikroskopie
Authors: Althoff T
History
DepositionFeb 15, 2011-
Header (metadata) releaseFeb 21, 2011-
Map releaseOct 12, 2011-
UpdateOct 12, 2011-
Current statusOct 12, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2ybb
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD1876_bt_m...

Downloads & links

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Map

FileDownload / File: emd_1876.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM map of supercomplex B (I1III2IV1) from bovine heart mitochondria
Voxel sizeX=Y=Z: 4.76 Å
Density
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-8.248889999999999 - 18.839099999999998
Average (Standard dev.)-0.00000000106836 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-56-56-55
Dimensions112112112
Spacing112112112
CellA=B=C: 533.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.764.764.76
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z533.120533.120533.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S213
start NC/NR/NS-56-56-55
NC/NR/NS112112112
D min/max/mean-8.24918.839-0.000

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Supplemental data

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Sample components

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Entire : Respiratory supercomplex B (I1III2IV1) composed of complex I, dim...

EntireName: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria
Components
  • Sample: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria
  • Protein or peptide: NADH-dehydrogenaseNADH dehydrogenase
  • Protein or peptide: Cytochrome c reductase
  • Protein or peptide: Cytochrome c oxidase
  • Protein or peptide: Cytochrome c

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Supramolecule #1000: Respiratory supercomplex B (I1III2IV1) composed of complex I, dim...

SupramoleculeName: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria
type: sample / ID: 1000
Details: The supercomplexes were kept soluble by amphipol A8-35
Oligomeric state: A monomer of complex I assembles with a dimer of complex III and a monomer of complex IV
Number unique components: 4
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: NADH-dehydrogenase

MacromoleculeName: NADH-dehydrogenase / type: protein_or_peptide / ID: 1 / Name.synonym: Complex I / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 980 KDa / Theoretical: 980 KDa

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Macromolecule #2: Cytochrome c reductase

MacromoleculeName: Cytochrome c reductase / type: protein_or_peptide / ID: 2 / Name.synonym: Complex III / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 243 KDa / Theoretical: 241 KDa

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Macromolecule #3: Cytochrome c oxidase

MacromoleculeName: Cytochrome c oxidase / type: protein_or_peptide / ID: 3 / Name.synonym: Complex IV / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 207 KDa / Theoretical: 204 KDa

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Macromolecule #4: Cytochrome c

MacromoleculeName: Cytochrome c / type: protein_or_peptide / ID: 4 / Name.synonym: Cytochrome c / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane
Molecular weightExperimental: 12 KDa / Theoretical: 12 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.7 / Details: 10 mM KCl, 15 mM HEPES, residual trehalose
GridDetails: Continuous carbon 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 95 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Custom-made hand plunger. Sample was adsorbed to carbon film for 30 seconds before blotting
Method: One-sided blotting for 26 - 30 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 58829 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: FEI Polara MSC / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -50
TemperatureMin: 78 K / Max: 95 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 x magnification
Legacy - Electron beam tilt params: Beam tilt was corrected by adjusting pivot points
DetailsLow dose conditions. For random conical tilt each area was imaged twice with the first image taken at a tilt angle of -45 or -50 degree
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 154 / Average electron dose: 25 e/Å2
Details: Scanned images were binned to 2.38 Angstroms per pixel in IMAGIC
Od range: 0.7 / Bits/pixel: 8
Tilt angle max0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase-flippping on each particle
Final angle assignmentDetails: SPIDER: theta 360 degrees, phi 360 degrees
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER, IMAGIC
Details: Final map was calculated from combined tilted and untilted datasets with 10684 projections each and omitting 30 per cent of images with lowest cross correlation coefficient using SIRT
Number images used: 10684
DetailsTilt pairs of particles were selected interactively in JWEB

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Atomic model buiding 1

Initial modelPDB ID:

3m9s

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Only one monomer from the asymmetric unit was used. Docking was done manually according to detailed map features
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 2

Initial modelPDB ID:

3iam

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Only one monomer from the asymmetric unit was used. Docking was done manually according to detailed map features. Gave better fit than
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 3

Initial modelPDB ID:

3m9c

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Docking was done manually according to detailed map features
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 4

Initial modelPDB ID:

1pp9

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Docking was done manually according to detailed map features
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 5

Initial modelPDB ID:

1bgy


Chain - #0 - Chain ID: K / Chain - #1 - Chain ID: W
SoftwareName: UCSF Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. Structure was aligned to PDB 1PP9 with Chimera MatchMaker
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 6

Initial modelPDB ID:

3cx5

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Structure was aligned to PDB 1PP9 with Chimera MatchMaker
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 7

Initial modelPDB ID:

2bcc

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Used for comparison of the conformation of the Rieske-domain. Structure was aligned to PDB 1PP9 with Chimera MatchMaker
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 8

Initial modelPDB ID:

1occ

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Only one monomer from the asymmetric unit was used. Docking was done manually according to detailed map features
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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Atomic model buiding 9

Initial modelPDB ID:

2b4z

SoftwareName: UCSF Chimera
DetailsProtocol: Rigid Body. Structure was aligned to cytochrome c (chain W) in PDB 3CX5 with Chimera Matchmaker
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2ybb:
Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)

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