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- EMDB-6774: Cryo-EM structure of human respiratory complex III (cytochrome bc... -

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Entry
Database: EMDB / ID: 6774
TitleCryo-EM structure of human respiratory complex III (cytochrome bc1 complex)
Map dataThis map was obtained by sub-region refinement.
SampleHuman respiratory complex III:
Function / homologyCytochrome c1 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b / Single alpha-helix domain superfamily / Cytochrome b/b6-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain ...Cytochrome c1 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b / Single alpha-helix domain superfamily / Cytochrome b/b6-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Rieske [2Fe-2S] iron-sulphur domain / Di-haem cytochrome, transmembrane / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Rieske iron-sulphur protein / Cytochrome c-like domain superfamily / Peptidase M16, N-terminal / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex subunit 9 / Peptidase M16, C-terminal / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, C-terminal / Peptidase M16, zinc-binding site / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex, subunit 6 / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Ubiquinol cytochrome reductase transmembrane region / Respiratory electron transport / Mitochondrial protein import / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6 N-terminal region profile. / Insulinase family, zinc-binding region signature. / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Peptidase M16 inactive domain / UcrQ family / Ubiquinol-cytochrome C reductase hinge protein / Insulinase (Peptidase family M16) / Cytochrome b-c1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6/petB / Rieske [2Fe-2S] domain / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome C1 family / Ubiquinol-cytochrome C reductase complex 14kD subunit / hyperosmotic salinity response / protein processing involved in protein targeting to mitochondrion / subthalamus development / pons development / mitochondrial respiratory chain complex III assembly / response to alkaloid / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / response to mercury ion / cerebellar Purkinje cell layer development / mitochondrial respiratory chain complex III / mitochondrial respiratory chain / oxidative phosphorylation / ubiquinol—cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial ATP synthesis coupled proton transport / electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity / integral component of mitochondrial inner membrane / mitochondrial respiratory chain complex IV / thalamus development / pyramidal neuron development / hypothalamus development / response to hormone / response to glucagon / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / midbrain development / response to copper ion / aerobic respiration / respiratory chain / response to hyperoxia / hippocampus development / protein processing / response to activity / generation of precursor metabolites and energy / 2 iron, 2 sulfur cluster binding / response to calcium ion / animal organ regeneration / metalloendopeptidase activity / mitochondrial inner membrane / response to heat / response to cadmium ion / oxidation-reduction process / response to ethanol / response to hypoxia / electron transfer activity / response to drug / myelin sheath / response to antibiotic
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.4 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: 5xte

SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Aug 30, 2017 / Last update: Sep 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0783
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0783
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xte
  • Surface level: 0.0783
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6774.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:0.0783 (by author), 0.0783 (movie #1):
Minimum - Maximum-0.17762329 - 0.33905625
Average (Standard dev.)0.00027273496 (0.005043188)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 519.83997 Å
α=β=γ: 90 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-0.1780.3390.000

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Supplemental data

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Sample components

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Entire Human respiratory complex III

EntireName: Human respiratory complex III / Details: Human cytochrome bc1 complex / Number of components: 1
MassExperimental: 500 kDa

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Component #1: protein, Human respiratory complex III

ProteinName: Human respiratory complex III / Details: Human cytochrome bc1 complex / Recombinant expression: No
MassExperimental: 500 kDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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