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- EMDB-6775: Cryo-EM structure of human respiratory supercomplex I1III2IV1 -

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Entry
Database: EMDB / ID: EMD-6775
TitleCryo-EM structure of human respiratory supercomplex I1III2IV1
Map data
SampleHuman respiratory supercomplex I1III2IV1
Function / homology
Function and homology information


positive regulation of peptidase activity / subthalamus development / pons development / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / hyperosmotic salinity response / Complex I biogenesis / cerebellar Purkinje cell layer development / TP53 Regulates Metabolic Genes ...positive regulation of peptidase activity / subthalamus development / pons development / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / hyperosmotic salinity response / Complex I biogenesis / cerebellar Purkinje cell layer development / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Respiratory electron transport / Cytoprotection by HMOX1 / Mitochondrial Fatty Acid Beta-Oxidation / mitochondrial respirasome assembly / response to mercury ion / oxidoreduction-driven active transmembrane transporter activity / pyramidal neuron development / cardiac muscle tissue development / respiratory chain complex IV / regulation of oxidative phosphorylation / response to alkaloid / Mitochondrial protein import / Respiratory electron transport / gliogenesis / mitochondrial respiratory chain complex III assembly / neural precursor cell proliferation / mitochondrial respiratory chain complex III / integral component of mitochondrial inner membrane / respiratory gaseous exchange by respiratory system / blastocyst hatching / thalamus development / NADH dehydrogenase activity / mitochondrial respirasome / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex IV / oxygen sensor activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / mitochondrial ribosome / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase / protein lipoylation / oxidative phosphorylation / Glyoxylate metabolism and glycine degradation / electron transport coupled proton transport / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / acyl binding / response to glucagon / sodium ion transport / cellular response to interferon-beta / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / mitochondrial translation / ATP synthesis coupled electron transport / ubiquinone binding / mitochondrial electron transport, cytochrome c to oxygen / azurophil granule membrane / NADH dehydrogenase (ubiquinone) activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / neurogenesis / midbrain development / hypothalamus development / quinone binding / apoptotic mitochondrial changes / response to copper ion / response to cobalamin / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / ATP metabolic process / proton transmembrane transport / RHOG GTPase cycle / aerobic respiration / cellular response to retinoic acid / respirasome / response to hyperoxia / extrinsic apoptotic signaling pathway / respiratory electron transport chain / substantia nigra development / fatty acid binding / negative regulation of intrinsic apoptotic signaling pathway / response to organonitrogen compound / animal organ regeneration / response to cAMP / synaptic membrane / cerebellum development / enzyme regulator activity / central nervous system development / mitochondrial membrane / regulation of mitochondrial membrane potential / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to glucose / apoptotic signaling pathway / response to nicotine / generation of precursor metabolites and energy / response to activity
Similarity search - Function
NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase 1 subunit C1 / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit ...NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase 1 subunit C1 / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Zinc-finger domain / Zinc finger, CHCC-type / GRIM-19 / GRIM-19 protein / Cytochrome c oxidase subunit VIIa, metazoa / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 / Cytochrome C oxidase, subunit VIIB / Cytochrome oxidase c subunit VIII / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 6C / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit Va/VI / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase subunit VIa / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit VIb superfamily / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase, subunit VIb / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, ESSS subunit / Cytochrome c oxidase subunit Vb / Cytochrome oxidase c subunit VIb / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / Cytochrome c oxidase subunit III domain / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, chain 2 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit I domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / NADH-ubiquinone oxidoreductase B12 subunit family / NADH-quinone oxidoreductase, chain I
Similarity search - Domain/homology
Cytochrome c oxidase subunit 8B, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial ...Cytochrome c oxidase subunit 8B, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c oxidase subunit 2 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Cytochrome b-c1 complex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Cytochrome c oxidase subunit 7C, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4 / Cytochrome c oxidase subunit 6B1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Cytochrome c oxidase subunit 5B, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome b / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGu J / Wu M / Yang M
CitationJournal: Cell / Year: 2017
Title: Architecture of Human Mitochondrial Respiratory Megacomplex IIIIIV.
Authors: Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang /
Abstract: The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, ...The respiratory megacomplex represents the highest-order assembly of respiratory chain complexes, and it allows mitochondria to respond to energy-requiring conditions. To understand its architecture, we examined the human respiratory chain megacomplex-IIIIIV (MCIIIIIV) with 140 subunits and a subset of associated cofactors using cryo-electron microscopy. The MCIIIIIV forms a circular structure with the dimeric CIII located in the center, where it is surrounded by two copies each of CI and CIV. Two cytochrome c (Cyt.c) molecules are positioned to accept electrons on the surface of the c state CIII dimer. Analyses indicate that CII could insert into the gaps between CI and CIV to form a closed ring, which we termed the electron transport chain supercomplex. The structure not only reveals the precise assignment of individual subunits of human CI and CIII, but also enables future in-depth analysis of the electron transport chain as a whole.
History
DepositionJun 18, 2017-
Header (metadata) releaseSep 13, 2017-
Map releaseSep 13, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-5xth
  • Surface level: 0.04
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6775.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 519.84 Å
1.08 Å/pix.
x 480 pix.
= 519.84 Å
1.08 Å/pix.
x 480 pix.
= 519.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density
Contour LevelBy AUTHOR: 0.0354 / Movie #1: 0.04
Minimum - Maximum-0.091495745 - 0.38491186
Average (Standard dev.)0.00086070073 (±0.0064994423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 519.83997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0831.0831.083
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z519.840519.840519.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0910.3850.001

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Supplemental data

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Sample components

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Entire Human respiratory supercomplex I1III2IV1

EntireName: Human respiratory supercomplex I1III2IV1 / Number of Components: 1

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Component #1: protein, Human respiratory supercomplex I1III2IV1

ProteinName: Human respiratory supercomplex I1III2IV1 / Recombinant expression: No
MassExperimental: 1.7 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.4
VitrificationCryogen Name: ETHANE

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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: 1.25 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 167761
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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