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- EMDB-6773: Cryo-EM structure of human respiratory complex I -

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Entry
Database: EMDB / ID: 6773
TitleCryo-EM structure of human respiratory complex I
Map dataThis map was obtained by sub-region refinement.
SampleHuman respiratory complex I:
Function / homologyNADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 ...NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Thioredoxin-like superfamily / 2Fe-2S ferredoxin-like superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Deoxynucleoside kinase domain / [NiFe]-hydrogenase, large subunit / P-loop containing nucleoside triphosphate hydrolase / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase 1 subunit C1 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Soluble ligand binding domain / Zinc finger, CHCC-type / NADH:ubiquinone oxidoreductase, 30kDa subunit / NAD-dependent epimerase/dehydratase / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-quinone oxidoreductase, chain M/4 / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase, subunit b14.5b / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone oxidoreductase, subunit G / NADH:ubiquinone oxidoreductase, B18 subunit / CHCH / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase subunit 5, C-terminal / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / Complex 1 LYR protein / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-quinone oxidoreductase subunit E-like / Acyl carrier protein (ACP) / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Molybdopterin oxidoreductase / ETC complex I subunit / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase, 4Fe-4S domain / Ribosomal protein/NADH dehydrogenase domain / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Phosphopantetheine attachment site. / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase 1 beta subcomplex subunit 2 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / 4Fe-4S dicluster domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / SLBB domain / Zinc-finger domain / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1.
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.7 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: 5xtd

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: 0.0525
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0525
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5xtd
  • Surface level: 0.0525
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6773.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:0.0525 (by author), 0.0525 (movie #1):
Minimum - Maximum-0.13369343 - 0.32487088
Average (Standard dev.)0.00051458186 (0.005860823)
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-0.1340.3250.001

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Supplemental data

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Sample components

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Entire Human respiratory complex I

EntireName: Human respiratory complex I / Number of components: 1
MassExperimental: 1000 kDa

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Component #1: protein, Human respiratory complex I

ProteinName: Human respiratory complex I / Recombinant expression: No
MassExperimental: 1000 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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