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- EMDB-4480: CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2 -

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Basic information

Entry
Database: EMDB / ID: EMD-4480
TitleCI Peripheral Arm focused refinement from Ovine respiratory SC I+III2
Map data
SampleOvine mitochondrial SC I+III2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 5
  • (NADH:ubiquinone oxidoreductase subunit ...) x 4
  • NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 5
  • Acyl carrier protein
  • (ligand) x 6
Function / homology
Function and homology information


blastocyst hatching / mitochondrial ATP synthesis coupled electron transport / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...blastocyst hatching / mitochondrial ATP synthesis coupled electron transport / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respirasome / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / circadian rhythm / negative regulation of cell growth / NAD binding / brain development / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / nuclear body / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 ...NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH dehydrogenase, subunit C / SLBB domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Epimerase domain-containing protein / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I subunit B13 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-30kD / Complex I-B14.5a / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial ...Epimerase domain-containing protein / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Complex I subunit B13 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-30kD / Complex I-B14.5a / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex I-B14
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLetts JA / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 18, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q9d
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4480.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 400 pix.
= 560. Å
1.4 Å/pix.
x 400 pix.
= 560. Å
1.4 Å/pix.
x 400 pix.
= 560. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.36786753 - 1.4292165
Average (Standard dev.)-0.00002810240 (±0.014591322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 560.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3681.429-0.000

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Supplemental data

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Segmentation: #1

Fileemd_4480_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Focused refinement around complex I peripheral arm. Half map 1

Fileemd_4480_half_map_1.map
AnnotationFocused refinement around complex I peripheral arm. Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Focused refinement around complex I peripheral arm. Half map 2

Fileemd_4480_half_map_2.map
AnnotationFocused refinement around complex I peripheral arm. Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ovine mitochondrial SC I+III2

EntireName: Ovine mitochondrial SC I+III2
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Number of Components: 25

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Component #1: protein, Ovine mitochondrial SC I+III2

ProteinName: Ovine mitochondrial SC I+III2
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Recombinant expression: No
MassTheoretical: 1.4 MDa
SourceSpecies: Ovis aries (sheep)
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane / Organ Or Tissue: Heart

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Component #2: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.678281 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #3: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.840428 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #4: protein, NADH:ubiquinone oxidoreductase core subunit S1

ProteinName: NADH:ubiquinone oxidoreductase core subunit S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 77.031156 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #5: protein, NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiq...

ProteinName: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.193273 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #6: protein, NADH:ubiquinone oxidoreductase core subunit S3

ProteinName: NADH:ubiquinone oxidoreductase core subunit S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.441793 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #7: protein, NADH:ubiquinone oxidoreductase core subunit S7

ProteinName: NADH:ubiquinone oxidoreductase core subunit S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.104531 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #8: protein, NADH:ubiquinone oxidoreductase core subunit S8

ProteinName: NADH:ubiquinone oxidoreductase core subunit S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.219947 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #9: protein, NADH:ubiquinone oxidoreductase subunit V3

ProteinName: NADH:ubiquinone oxidoreductase subunit V3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.423314 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #10: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.651796 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #11: protein, NADH:ubiquinone oxidoreductase subunit S4

ProteinName: NADH:ubiquinone oxidoreductase subunit S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.3753 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #12: protein, NADH:ubiquinone oxidoreductase subunit A9

ProteinName: NADH:ubiquinone oxidoreductase subunit A9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.660488 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #13: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.966627 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #14: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.156311 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #15: protein, NADH:ubiquinone oxidoreductase subunit A6

ProteinName: NADH:ubiquinone oxidoreductase subunit A6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.923245 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #16: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.399201 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #17: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.115508 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #18: protein, Acyl carrier protein

ProteinName: Acyl carrier protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.119541 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #19: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Details: This is a focused refinement so only the N-terminal part of this subunit is present in the map.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.635264 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #20: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #21: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

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Component #22: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #24: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

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Component #25: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL
Buffer solution: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: PROPANE / Temperature: 277 K / Humidity: 95 %
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 51 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 1854

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 178121
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.8 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1LNK
Overall BValue: 90
Output model

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