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

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Entry
Database: EMDB / ID: 6771
TitleCryo-EM structure of human respiratory complex I matrix arm
Map dataThis map was obtained by sub-region refinemet
SampleHuman respiratory complex I matrix arm:
Function / homologyMolybdopterin oxidoreductase / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Zinc finger, CHCC-type ...Molybdopterin oxidoreductase / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Zinc finger, CHCC-type / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase flavoprotein 3 / [NiFe]-hydrogenase, large subunit / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, subunit G / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NAD-dependent epimerase/dehydratase / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / ETC complex I subunit / NADH-quinone oxidoreductase, chain I / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / Molybdopterin oxidoreductase, 4Fe-4S domain / Ribosomal protein/NADH dehydrogenase domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex 1 LYR protein / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase subunit B14.5a / NADH dehydrogenase, subunit C / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D superfamily / Carrier protein (CP) domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / 4Fe-4S dicluster domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Molybdopterin oxidoreductase / Phosphopantetheine attachment site / NADH ubiquinone oxidoreductase, 20 Kd subunit / NAD dependent epimerase/dehydratase family / Respiratory-chain NADH dehydrogenase 51 Kd subunit / ETC complex I subunit conserved region / ETC complex I subunit conserved region / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NADH ubiquinone oxidoreductase subunit NDUFA12 / Complex 1 protein (LYR family) / GRIM-19 protein / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Zinc-finger domain / SLBB domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / positive regulation of peptidase activity / ubiquinone-6 biosynthetic process / reproductive system development / protein import into mitochondrial inner membrane / NADH dehydrogenase (ubiquinone) / NADH dehydrogenase / mitochondrial respiratory chain complex I / mitochondrial ribosome / NADH dehydrogenase activity
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: 5xtb

SummaryFull reportAbout validation report
DateDeposition: Jun 17, 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: 0.0516
  • Imaged by UCSF Chimera
  • Download
  • 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

Downloads & links

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Map

Fileemd_6771.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:0.0516 (by author), 0.0516 (movie #1):
Minimum - Maximum-0.19345994 - 0.6161111
Average (Standard dev.)0.00020600946 (0.00461766)
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-0.1930.6160.000

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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

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