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

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Entry
Database: EMDB / ID: 6775
TitleCryo-EM structure of human respiratory supercomplex I1III2IV1
Map data
SampleHuman respiratory supercomplex I1III2IV1:
Function / homologyNADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase, subunit b14.5b / GRIM-19 / Phosphopantetheine binding ACP domain / Cupredoxin / NADH:ubiquinone oxidoreductase, B18 subunit / NADH-quinone oxidoreductase, chain I ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase, subunit b14.5b / GRIM-19 / Phosphopantetheine binding ACP domain / Cupredoxin / NADH:ubiquinone oxidoreductase, B18 subunit / NADH-quinone oxidoreductase, chain I / Cytochrome C oxidase, subunit VIIB / Cytochrome b-c1 complex subunit 9 / Complex 1 LYR protein / Peptidase M16, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Ribosomal protein/NADH dehydrogenase domain / Molybdopterin oxidoreductase, 4Fe-4S domain / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain M/4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Peptidase M16, N-terminal / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit II / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit IV / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, MNLL subunit / Cytochrome C oxidase subunit II, transmembrane domain / NADH:ubiquinone oxidoreductase, subunit G / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH ubiquinone oxidoreductase, F subunit / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 2, C-terminal / CHCH / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c1 / Cytochrome c oxidase, subunit Vb / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / Cytochrome c oxidase, subunit Va/VI / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NAD-dependent epimerase/dehydratase / Copper centre Cu(A) / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / Peptidase M16, zinc-binding site / Cytochrome c oxidase, subunit VIa / NADH:ubiquinone oxidoreductase, 30kDa subunit / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase, subunit 8 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase subunit 6C / Phosphopantetheine attachment site / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, chain 2 / Cytochrome b-c1 complex, subunit 6 / Acyl carrier protein (ACP) / Cytochrome b-c1 complex subunit 10 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase chain 4L/K / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome c oxidase, subunit VIa superfamily / NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome b/b6, C-terminal domain superfamily / 2Fe-2S ferredoxin-like superfamily / Cytochrome c oxidase subunit III-like superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit IV superfamily / Deoxynucleoside kinase domain / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
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.
Validation ReportPDB-ID: 5xth

SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Dec 13, 2017

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

Downloads & links

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Map

Fileemd_6775.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
1.08 Å/pix.
= 519.84 Å
480 pix
1.08 Å/pix.
= 519.84 Å
480 pix
1.08 Å/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 Level:0.0354 (by author), 0.04 (movie #1):
Minimum - Maximum-0.091495745 - 0.38491186
Average (Standard dev.)0.00086070073 (0.0064994423)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin0.00.00.0
Limit479.0479.0479.0
Spacing480480480
CellA=B=C: 519.83997 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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