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- EMDB-9534: Architecture of mammalian respirasome -

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Basic information

Entry
Database: EMDB / ID: 9534
TitleArchitecture of mammalian respirasome
Map data
SampleRespirasome
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • NADH-ubiquinone oxidoreductase 75 kDa subunit
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • Acyl carrier protein
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 3
  • Mitochondrial NADH dehydrogenase Fe-S protein 4
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 unknown subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (ligand) x 10
Function / homologyCytochrome c oxidase-like, subunit I domain / NADH-ubiquinone oxidoreductase, subunit 10 / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Rieske [2Fe-2S] iron-sulphur domain ...Cytochrome c oxidase-like, subunit I domain / NADH-ubiquinone oxidoreductase, subunit 10 / Cytochrome b-c1 complex subunit 10 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Rieske [2Fe-2S] iron-sulphur domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Cytochrome c oxidase, subunit VIa, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / Zinc finger, CHCC-type / Cytochrome c oxidase, subunit II / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c1, transmembrane anchor, C-terminal / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Protein MGARP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Cytochrome b/b6-like domain superfamily / Rieske iron-sulphur protein / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / [NiFe]-hydrogenase, large subunit / Cupredoxin / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Molybdopterin oxidoreductase / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase, 4Fe-4S domain / Peptidase M16, C-terminal / Complex 1 LYR protein / Cytochrome b-c1 complex subunit 9 / NmrA-like domain / Cytochrome C oxidase, subunit VIIB / Cytochrome c-like domain / Cytochrome c oxidase subunit IV / Phosphopantetheine binding ACP domain / GRIM-19 / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit G / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase subunit 5, C-terminal / Globular protein, non-globular alpha/beta subunit / Metalloenzyme, LuxS/M16 peptidase-like / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Cytochrome C oxidase subunit II, transmembrane domain / Peptidase M16, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Single alpha-helix domain superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Phosphopantetheine attachment site / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6/petB / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Rieske [2Fe-2S] domain / Proton-conducting membrane transporter / Molybdopterin oxidoreductase / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, subunit D superfamily / Insulinase (Peptidase family M16) / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / Cytochrome c oxidase subunit Vb / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Deoxynucleoside kinase / Cytochrome c oxidase subunit VIa / Cytochrome C1 family / Cytochrome c oxidase subunit Va / Cytochrome oxidase c subunit VIII / Cytochrome oxidase c subunit VIb / Ubiquinol-cytochrome C reductase hinge protein / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Cytochrome b / Cytochrome c oxidase, subunit Va/VI superfamily / Deoxynucleoside kinase domain / Protein MGARP, N-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase subunit 2, C-terminal / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome b/b6, C-terminal domain superfamily
Function and homology information
SourceSus scrofa (pig) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 5.4 Å resolution
AuthorsGu J / Wu M
CitationJournal: Nature / Year: 2016
Title: The architecture of the mammalian respirasome.
Authors: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang
Validation ReportPDB-ID: 5gpn

SummaryFull reportAbout validation report
DateDeposition: Oct 31, 2016 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 12, 2017 / Last update: Apr 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5gpn
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9534.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.05 Å/pix.
= 505.421 Å
480 pix
1.05 Å/pix.
= 505.421 Å
480 pix
1.05 Å/pix.
= 505.421 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05296 Å
Density
Contour Level:0.0216 (by author), 0.0216 (movie #1):
Minimum - Maximum-0.04734845 - 0.11140665
Average (Standard dev.)0.0005272059 (0.003714595)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 505.4208 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.05296041666671.05296041666671.0529604166667
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z505.421505.421505.421
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0470.1110.001

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Supplemental data

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Sample components

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Entire Respirasome

EntireName: Respirasome / Details: Mammalian, respirasome / Number of components: 74
MassExperimental: 1.7 MDa

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Component #1: protein, Respirasome

ProteinName: Respirasome / Details: Mammalian, respirasome / Recombinant expression: No
MassExperimental: 1.7 MDa
SourceSpecies: Sus scrofa (pig)

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Component #2: protein, Cytochrome b-c1 complex subunit 1, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Recombinant expression: No
MassTheoretical: 49.266254 kDa
SourceSpecies: Bos taurus (cattle)

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Component #3: protein, Cytochrome b-c1 complex subunit 2, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrial / Recombinant expression: No
MassTheoretical: 46.575469 kDa
SourceSpecies: Bos taurus (cattle)

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Component #4: protein, Cytochrome b

ProteinName: Cytochrome b / Recombinant expression: No
MassTheoretical: 42.62034 kDa
SourceSpecies: Bos taurus (cattle)

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Component #5: protein, Cytochrome c1, heme protein, mitochondrial

ProteinName: Cytochrome c1, heme protein, mitochondrial / Recombinant expression: No
MassTheoretical: 27.323277 kDa
SourceSpecies: Bos taurus (cattle)

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Component #6: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Recombinant expression: No
MassTheoretical: 29.572814 kDa
SourceSpecies: Bos taurus (cattle)

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Component #7: protein, Cytochrome b-c1 complex subunit 7

ProteinName: Cytochrome b-c1 complex subunit 7 / Recombinant expression: No
MassTheoretical: 13.37119 kDa
SourceSpecies: Bos taurus (cattle)

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Component #8: protein, Cytochrome b-c1 complex subunit 8

ProteinName: Cytochrome b-c1 complex subunit 8 / Recombinant expression: No
MassTheoretical: 9.606027 kDa
SourceSpecies: Bos taurus (cattle)

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Component #9: protein, Cytochrome b-c1 complex subunit 6, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 6, mitochondrial / Recombinant expression: No
MassTheoretical: 9.189116 kDa
SourceSpecies: Bos taurus (cattle)

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Component #10: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Recombinant expression: No
MassTheoretical: 7.964259 kDa
SourceSpecies: Bos taurus (cattle)

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Component #11: protein, Cytochrome b-c1 complex subunit 9

ProteinName: Cytochrome b-c1 complex subunit 9 / Recombinant expression: No
MassTheoretical: 7.209311 kDa
SourceSpecies: Bos taurus (cattle)

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Component #12: protein, Cytochrome b-c1 complex subunit 10

ProteinName: Cytochrome b-c1 complex subunit 10 / Recombinant expression: No
MassTheoretical: 6.527604 kDa
SourceSpecies: Bos taurus (cattle)

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Component #13: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Recombinant expression: No
MassTheoretical: 30.241416 kDa
SourceSpecies: Sus scrofa (pig)

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Component #14: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit / Recombinant expression: No
MassTheoretical: 79.627398 kDa
SourceSpecies: Sus scrofa (pig)

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Component #15: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / Recombinant expression: No
MassTheoretical: 52.552301 kDa
SourceSpecies: Sus scrofa (pig)

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Component #16: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7 / Recombinant expression: No
MassTheoretical: 23.777742 kDa
SourceSpecies: Sus scrofa (pig)

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Component #17: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8 / Recombinant expression: No
MassTheoretical: 23.893281 kDa
SourceSpecies: Sus scrofa (pig)

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Component #18: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Recombinant expression: No
MassTheoretical: 50.637766 kDa
SourceSpecies: Sus scrofa (pig)

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Component #19: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Recombinant expression: No
MassTheoretical: 27.439533 kDa
SourceSpecies: Sus scrofa (pig)

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Component #20: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Recombinant expression: No
MassTheoretical: 35.66752 kDa
SourceSpecies: Sus scrofa (pig)

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Component #21: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Recombinant expression: No
MassTheoretical: 39.077504 kDa
SourceSpecies: Sus scrofa (pig)

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Component #22: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Recombinant expression: No
MassTheoretical: 12.998448 kDa
SourceSpecies: Sus scrofa (pig)

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Component #23: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Recombinant expression: No
MassTheoretical: 51.859387 kDa
SourceSpecies: Sus scrofa (pig)

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Component #24: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Recombinant expression: No
MassTheoretical: 10.827253 kDa
SourceSpecies: Sus scrofa (pig)

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Component #25: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Recombinant expression: No
MassTheoretical: 68.6955 kDa
SourceSpecies: Sus scrofa (pig)

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Component #26: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Recombinant expression: No
MassTheoretical: 19.021332 kDa
SourceSpecies: Sus scrofa (pig)

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Recombinant expression: No
MassTheoretical: 9.225567 kDa
SourceSpecies: Sus scrofa (pig)

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Component #28: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Recombinant expression: No
MassTheoretical: 11.099798 kDa
SourceSpecies: Sus scrofa (pig)

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Component #29: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Recombinant expression: No
MassTheoretical: 12.506591 kDa
SourceSpecies: Sus scrofa (pig)

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
Recombinant expression: No
MassTheoretical: 42.606324 kDa
SourceSpecies: Sus scrofa (pig)

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Component #31: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Recombinant expression: No
MassTheoretical: 40.476082 kDa
SourceSpecies: Sus scrofa (pig)

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Component #32: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Recombinant expression: No
MassTheoretical: 16.911611 kDa
SourceSpecies: Sus scrofa (pig)

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Component #33: protein, Acyl carrier protein

ProteinName: Acyl carrier protein / Recombinant expression: No
MassTheoretical: 17.326223 kDa
SourceSpecies: Sus scrofa (pig)

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Component #34: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
Recombinant expression: No
MassTheoretical: 21.587006 kDa
SourceSpecies: Sus scrofa (pig)

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Component #35: protein, Mitochondrial NADH dehydrogenase Fe-S protein 4

ProteinName: Mitochondrial NADH dehydrogenase Fe-S protein 4 / Recombinant expression: No
MassTheoretical: 19.7185 kDa
SourceSpecies: Sus scrofa (pig)

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Component #36: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Recombinant expression: No
MassTheoretical: 13.34895 kDa
SourceSpecies: Sus scrofa (pig)

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Component #37: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Recombinant expression: No
MassTheoretical: 29.9436 kDa
SourceSpecies: Bos taurus (cattle)

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Component #38: protein, Cytochrome c oxidase subunit 4 isoform 1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
Recombinant expression: No
MassTheoretical: 17.179646 kDa
SourceSpecies: Bos taurus (cattle)

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Component #39: protein, Cytochrome c oxidase subunit 5A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5A, mitochondrial / Recombinant expression: No
MassTheoretical: 12.453081 kDa
SourceSpecies: Bos taurus (cattle)

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Component #40: protein, Cytochrome c oxidase subunit 5B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 5B, mitochondrial / Recombinant expression: No
MassTheoretical: 10.684038 kDa
SourceSpecies: Bos taurus (cattle)

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Component #41: protein, Cytochrome c oxidase subunit 6A2, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6A2, mitochondrial / Recombinant expression: No
MassTheoretical: 9.452687 kDa
SourceSpecies: Bos taurus (cattle)

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Component #42: protein, Cytochrome c oxidase subunit 6B1

ProteinName: Cytochrome c oxidase subunit 6B1 / Recombinant expression: No
MassTheoretical: 10.039244 kDa
SourceSpecies: Bos taurus (cattle)

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Component #43: protein, Cytochrome c oxidase subunit 6C

ProteinName: Cytochrome c oxidase subunit 6C / Recombinant expression: No
MassTheoretical: 8.494982 kDa
SourceSpecies: Bos taurus (cattle)

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Component #44: protein, Cytochrome c oxidase subunit 7A1, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7A1, mitochondrial / Recombinant expression: No
MassTheoretical: 6.682726 kDa
SourceSpecies: Bos taurus (cattle)

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Component #45: protein, Cytochrome c oxidase subunit 7B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7B, mitochondrial / Recombinant expression: No
MassTheoretical: 6.365217 kDa
SourceSpecies: Bos taurus (cattle)

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Component #46: protein, Cytochrome c oxidase subunit 7C, mitochondrial

ProteinName: Cytochrome c oxidase subunit 7C, mitochondrial / Recombinant expression: No
MassTheoretical: 5.449396 kDa
SourceSpecies: Bos taurus (cattle)

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Component #47: protein, Cytochrome c oxidase subunit 8B, mitochondrial

ProteinName: Cytochrome c oxidase subunit 8B, mitochondrial / Recombinant expression: No
MassTheoretical: 4.967756 kDa
SourceSpecies: Bos taurus (cattle)

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Component #48: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Recombinant expression: No
MassTheoretical: 57.065844 kDa
SourceSpecies: Bos taurus (cattle)

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Component #49: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Recombinant expression: No
MassTheoretical: 26.040393 kDa
SourceSpecies: Bos taurus (cattle)

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Component #50: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 11.422071 kDa
SourceSpecies: Sus scrofa (pig)

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Component #51: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 8.088424 kDa
SourceSpecies: Sus scrofa (pig)

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Component #52: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 3.677524 kDa
SourceSpecies: Sus scrofa (pig)

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Component #53: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Recombinant expression: No
MassTheoretical: 13.32159 kDa
SourceSpecies: Sus scrofa (pig)

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Component #54: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 14.953313 kDa
SourceSpecies: Sus scrofa (pig)

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Component #55: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Recombinant expression: No
MassTheoretical: 14.686894 kDa
SourceSpecies: Sus scrofa (pig)

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Component #56: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Recombinant expression: No
MassTheoretical: 20.944768 kDa
SourceSpecies: Sus scrofa (pig)

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Component #57: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Recombinant expression: No
MassTheoretical: 21.733711 kDa
SourceSpecies: Sus scrofa (pig)

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Component #58: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / Recombinant expression: No
MassTheoretical: 14.327655 kDa
SourceSpecies: Sus scrofa (pig)

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Component #59: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1 / Recombinant expression: No
MassTheoretical: 8.630037 kDa
SourceSpecies: Sus scrofa (pig)

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Component #60: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Recombinant expression: No
MassTheoretical: 20.064096 kDa
SourceSpecies: Sus scrofa (pig)

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Component #61: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 6.485986 kDa
SourceSpecies: Sus scrofa (pig)

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Component #62: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 2.91158 kDa
SourceSpecies: Sus scrofa (pig)

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Component #63: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 1.464797 kDa
SourceSpecies: Sus scrofa (pig)

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Component #64: protein, NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment

ProteinName: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Recombinant expression: No
MassTheoretical: 1.124378 kDa
SourceSpecies: Sus scrofa (pig)

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Component #65: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #66: ligand, HEME C

LigandName: HEME C / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.618503 kDa

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Component #67: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #68: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTER / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #69: ligand, FLAVIN MONONUCLEOTIDE

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

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Component #70: 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 #71: ligand, ZINC ION

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

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Component #72: ligand, HEME-A

LigandName: HEME-A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.852837 kDa

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Component #73: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

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Component #74: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 139996
3D reconstructionSoftware: EMAN / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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About Yorodumi

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News

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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. See below links for details.
  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

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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.

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

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