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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 ...Coenzyme Q – cytochrome c reductase) 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/homologyMitochondrial Fatty Acid Beta-Oxidation / Protein MGARP, N-terminal / Protein MGARP / Complex I biogenesis / Respiratory electron transport / Mitochondria Localisation Sequence / Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24 / ubiquinone-6 biosynthetic process / Glyoxylate metabolism and glycine degradation / Tim17/Tim22/Tim23/Pmp24 family ...Mitochondrial Fatty Acid Beta-Oxidation / Protein MGARP, N-terminal / Protein MGARP / Complex I biogenesis / Respiratory electron transport / Mitochondria Localisation Sequence / Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24 / ubiquinone-6 biosynthetic process / Glyoxylate metabolism and glycine degradation / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / GRIM-19 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / GRIM-19 protein / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Zinc finger, CHCC-type / reproductive system development / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-quinone oxidoreductase, chain M/4 / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH-plastoquinone oxidoreductase, chain 5 / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH dehydrogenase (ubiquinone) / ETC complex I subunit conserved region / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase subunit E-like / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Complex 1 LYR protein / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, subunit D / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH dehydrogenase subunit 5 C-terminus / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase subunit 2 C-terminus / mitochondrial respiratory chain complex I / Soluble ligand binding domain / intrinsic component of mitochondrial membrane / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Zinc-finger domain / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH dehydrogenase / NmrA-like domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / CHCH / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH dehydrogenase activity / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / mitochondrial respiratory chain complex I assembly / protein processing involved in protein targeting to mitochondrion / subthalamus development / mitochondrial electron transport, NADH to ubiquinone / pons development / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome c oxidase, subunit VIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit 8
Function and homology information
SourceSus scrofa / Wild boar / mammal / image: Sus scrofa domestica
Bos taurus / Cattle / mammal /
MethodCryo EM / single particle reconstruction / 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
Abstract: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.
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
3D viewer
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 package.

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

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

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrialCoenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 49.266254 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrialCoenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 46.575469 kDa
SourceSpecies: Bos taurus

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Component #4: protein, Cytochrome b

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

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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

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

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrialCoenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 29.572814 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 7Coenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 13.37119 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 8Coenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 9.606027 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 6, mitochondrialCoenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 9.189116 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrialCoenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 7.964259 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 9Coenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 7.209311 kDa
SourceSpecies: Bos taurus

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

ProteinName: Cytochrome b-c1 complex subunit 10Coenzyme Q – cytochrome c reductase
Recombinant expression: No
MassTheoretical: 6.527604 kDa
SourceSpecies: Bos taurus

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Component #33: protein, Acyl carrier protein

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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
SourceSpecies:

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Component #66: ligand, HEME C

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

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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
SourceSpecies:

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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
SourceSpecies:

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Component #69: ligand, FLAVIN MONONUCLEOTIDE

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

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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
SourceSpecies:

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Component #71: ligand, ZINC ION

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

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Component #72: ligand, HEME-A

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

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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
SourceSpecies:

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Component #74: ligand, MAGNESIUM ION

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

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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

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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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.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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