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- EMDB-6771: Cryo-EM structure of human respiratory complex I matrix arm -

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Basic information

Entry
Database: EMDB / ID: EMD-6771
TitleCryo-EM structure of human respiratory complex I matrix arm
Map data
SampleHuman respiratory complex I matrix arm
Function / homology
Function and homology information


positive regulation of peptidase activity / 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 / Respiratory electron transport / gliogenesis / neural precursor cell proliferation ...positive regulation of peptidase activity / 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 / 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 / mitochondrial ribosome / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / protein lipoylation / Glyoxylate metabolism and glycine degradation / mitochondrial respiratory chain complex I / electron transport coupled proton transport / 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 / NADH dehydrogenase (ubiquinone) activity / neurogenesis / quinone binding / apoptotic mitochondrial changes / reactive oxygen species metabolic process / ATP metabolic process / RHOG GTPase cycle / aerobic respiration / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / respiratory electron transport chain / substantia nigra development / fatty acid binding / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / synaptic membrane / mitochondrial membrane / regulation of mitochondrial membrane potential / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to glucose / apoptotic signaling pathway / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / positive regulation of protein catabolic process / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / nervous system development / brain development / mitochondrial inner membrane / response to oxidative stress / protease binding / nuclear body / structural constituent of ribosome / electron transfer activity / mitochondrial matrix / neuron projection / negative regulation of transcription, DNA-templated / neuronal cell body / protein-containing complex binding / ubiquitin protein ligase binding / calcium ion binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Zinc-finger domain / Zinc finger, CHCC-type / GRIM-19 protein / GRIM-19 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-quinone oxidoreductase, chain I ...NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Zinc-finger domain / Zinc finger, CHCC-type / GRIM-19 protein / GRIM-19 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-quinone oxidoreductase, chain I / 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, 49kDa subunit, conserved site / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-quinone oxidoreductase, subunit D / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / 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 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH dehydrogenase, subunit C / NADH-quinone oxidoreductase subunit E-like / SLBB domain / Soluble ligand binding domain / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 30kDa subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Complex 1 protein (LYR family) / Complex 1 LYR protein domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Phosphopantetheine attachment site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 ...NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 17, 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: 0.0516
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0516
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5xtb
  • Surface level: 0.0516
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6771.png

Downloads & links

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Map

FileDownload / File: emd_6771.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0516 / Movie #1: 0.0516
Minimum - Maximum-0.19345994 - 0.6161111
Average (Standard dev.)0.00020600946 (±0.00461766)
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-0.1930.6160.000

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Supplemental data

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Sample components

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Entire Human respiratory complex I matrix arm

EntireName: Human respiratory complex I matrix arm / Number of Components: 1

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Component #1: protein, Human respiratory complex I matrix arm

ProteinName: Human respiratory complex I matrix arm / Recombinant expression: No
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.: 0.4 mg/mL / pH: 7.4
VitrificationCryogen Name: ETHANE / Humidity: 100 %

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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

5xtb

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