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- EMDB-6772: Cryo-EM structure of human respiratory complex I transmembrane arm -

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Entry
Database: EMDB / ID: 6772
TitleCryo-EM structure of human respiratory complex I transmembrane arm
Map dataThis map was obtained by sub-region refinement.
SampleHuman respiratory complex I transmembrane arm:
Function / homologyNADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 ...NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Deoxynucleoside kinase domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase subunit 5, C-terminal / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, chain 2 / Acyl carrier protein (ACP) / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone oxidoreductase chain 4, N-terminal / CHCH / Phosphopantetheine attachment site / Complex 1 LYR protein / NADH:ubiquinone oxidoreductase, B18 subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase, subunit b14.5b / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-quinone oxidoreductase, chain M/4 / ACP-like superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / Phosphopantetheine attachment site. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Carrier protein (CP) domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Neutrophil degranulation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Proton-conducting membrane transporter / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Phosphopantetheine attachment site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4, amino terminus / Deoxynucleoside kinase / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / MNLL subunit / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH dehydrogenase subunit 2 C-terminus / NADH dehydrogenase subunit 5 C-terminus / CHCH domain / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / response to light intensity / positive regulation of peptidase activity / protein import into mitochondrial inner membrane / NADH dehydrogenase (ubiquinone) / NADH dehydrogenase / mitochondrial respiratory chain complex I / NADH dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / protein lipoylation / cellular respiration
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: 5xtc

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: 0.0677
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0677
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5xtc
  • Surface level: 0.0677
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6772.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:0.0677 (by author), 0.0677 (movie #1):
Minimum - Maximum-0.15407616 - 0.305299
Average (Standard dev.)0.00037028454 (0.005278367)
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-0.1540.3050.000

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Supplemental data

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Sample components

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Entire Human respiratory complex I transmembrane arm

EntireName: Human respiratory complex I transmembrane arm / Number of components: 1

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

ProteinName: Human respiratory complex I transmembrane 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.: 0.2 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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