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

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Basic information

Entry
Database: EMDB / ID: EMD-6773
TitleCryo-EM structure of human respiratory complex I
Map data
SampleHuman respiratory complex I
Function / homology
Function and homology information


positive regulation of peptidase activity / response to light intensity / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / cardiac muscle tissue development / Mitochondrial protein import / Respiratory electron transport ...positive regulation of peptidase activity / response to light intensity / ubiquinone-6 biosynthetic process / protein insertion into mitochondrial inner membrane / cellular response to oxygen levels / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / cardiac muscle tissue development / Mitochondrial protein import / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / respiratory gaseous exchange by respiratory system / blastocyst hatching / NADH dehydrogenase activity / mitochondrial respirasome / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / oxygen sensor activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / mitochondrial ribosome / protein lipoylation / Glyoxylate metabolism and glycine degradation / electron transport coupled proton transport / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / acyl binding / 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 / response to hydroperoxide / ubiquinone binding / azurophil granule membrane / NADH dehydrogenase (ubiquinone) activity / cellular response to glucocorticoid stimulus / neurogenesis / quinone binding / apoptotic mitochondrial changes / ionotropic glutamate receptor binding / reactive oxygen species metabolic process / ATP metabolic process / RHOG GTPase cycle / aerobic respiration / cellular response to retinoic acid / respirasome / extrinsic apoptotic signaling pathway / respiratory electron transport chain / substantia nigra development / fatty acid binding / response to cocaine / negative regulation of intrinsic apoptotic signaling pathway / response to organonitrogen compound / response to cAMP / synaptic membrane / cerebellum 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 / regulation of protein phosphorylation / sensory perception of sound / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / response to organic cyclic compound / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / response to hydrogen peroxide / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / nervous system development / brain development / mitochondrial inner membrane / response to oxidative stress / in utero embryonic development / response to ethanol / protease binding / nuclear body / postsynaptic density / structural constituent of ribosome / response to hypoxia / electron transfer activity / aging / mitochondrial matrix / nuclear speck / neuron projection / negative regulation of transcription, DNA-templated / neuronal cell body / response to xenobiotic stimulus => GO:0009410 / dendrite / protein-containing complex binding
Similarity search - Function
NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / 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 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / 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 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH-quinone oxidoreductase, chain I / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase subunit D/H / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Deoxynucleoside kinase / Deoxynucleoside kinase domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase / Soluble ligand binding domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / SLBB domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial ...NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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) releaseAug 30, 2017-
Map releaseAug 30, 2017-
UpdateSep 6, 2017-
Current statusSep 6, 2017Processing site: PDBj / Status: Released

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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
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6773.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: 0.0525 / Movie #1: 0.0525
Minimum - Maximum-0.13369343 - 0.32487088
Average (Standard dev.)0.00051458186 (±0.005860823)
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-0.1340.3250.001

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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

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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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