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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 dataThis map was obtained by sub-region refinemet
Sample
  • Complex: Human respiratory complex I matrix arm
Function / homology
Function and homology information


protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / ubiquinone biosynthetic process / cellular respiration / cellular response to oxygen levels ...protein lipoylation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / ubiquinone biosynthetic process / cellular respiration / cellular response to oxygen levels / mesenchymal stem cell proliferation / respiratory chain complex / mitochondrial [2Fe-2S] assembly complex / reproductive system development / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / mesenchymal stem cell differentiation / circulatory system development / regulation of protein phosphorylation / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cardiac muscle tissue development / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / stem cell division / sodium ion transport / NADH dehydrogenase activity / iron-sulfur cluster assembly / acyl binding / mitochondrial ATP synthesis coupled electron transport / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / RHOG GTPase cycle / positive regulation of execution phase of apoptosis / respiratory chain complex I / response to cAMP / NADH dehydrogenase (ubiquinone) activity / endopeptidase activator activity / quinone binding / cellular response to interferon-beta / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / neurogenesis / regulation of mitochondrial membrane potential / substantia nigra development / Mitochondrial protein degradation / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / synaptic membrane / fatty acid binding / respiratory electron transport chain / DNA damage response, signal transduction by p53 class mediator / kidney development / fatty acid metabolic process / monooxygenase activity / circadian rhythm / mitochondrial membrane / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / NAD binding / positive regulation of protein catabolic process / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / protease binding / gene expression / electron transfer activity / mitochondrial inner membrane / nuclear body / mitochondrial matrix / neuronal cell body / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / structural molecule activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Complex1_LYR-like / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Zinc finger, CHCC-type / Zinc-finger domain ...Complex1_LYR-like / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 / GRIM-19 protein / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / 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 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / 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 / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 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) / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / 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 / 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] iron-sulfur protein 8, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / 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] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / 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] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha 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] 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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / 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)
AnnotationThis map was obtained by sub-region refinemet
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
Components
  • Complex: Human respiratory complex I matrix arm

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Supramolecule #1: Human respiratory complex I matrix arm

SupramoleculeName: Human respiratory complex I matrix arm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 167761
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)

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