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Cryo-EM structure of human respiratory complex I transmembrane arm

by single particle reconstruction, at 3.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0677, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0677, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5xtc, Surface level: 0.0677, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 6772
TitleCryo-EM structure of human respiratory complex I transmembrane arm
MapThis map was obtained by sub-region refinement.
SampleHuman respiratory complex I transmembrane arm
AuthorsGu J, Wu M, Yang M
DateDeposition: 2017-06-18, Header release: 2017-08-30, Map release: 2017-08-30, Last update: 2017-09-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0677, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0677, Imaged by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-5xtc, Surface level: 0.0677, Imaged by UCSF CHIMERA

Supplemental images
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Related Structure Data
Related Entries

PDB-5xtc

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleCell, Vol. 170, Issue 6, Page 1247-1257.e12, Year 2017
TitleArchitecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
AuthorsRunyu Guo, Shuai Zong, Meng Wu, Jinke Gu, Maojun Yang
Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.
KeywordsCryoelectron Microscopy, Electron Transport Chain Complex Proteins (chemistry), Electron Transport Complex I (chemistry, 1.6.5.3), Electron Transport Complex II (chemistry, 1.3.5.1), Humans, Mitochondria (chemistry), Models, Molecular, Multienzyme Complexes (chemistry), respiratory complex II (1.6.5.3)
LinksPubMed: 28844695, PII: S0092-8674(17)30887-5, DOI: 10.1016/j.cell.2017.07.050
Map
Fileemd_6772.map.gz ( map file in CCP4 format, 442369 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.083 A/pix
= 519.84 A
480 pix
1.083 A/pix
= 519.84 A
480 pix
1.083 A/pix
= 519.84 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0677 (by author), 0.0677 (movie #1):
Minimum - Maximum: -0.15407616 - 0.305299
Average (Standard dev.): 0.00037028454 (0.005278367)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
Unit CellA= B= C: 519.83997 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.083 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.1540.3050.000
Annotation DetailsThis map was obtained by sub-region refinement.
Supplement
Images
Images
Sample
NameHuman respiratory complex I transmembrane arm
Number of Components1
Component #1: protein - Human respiratory complex I transmembrane arm
Scientific nameHuman respiratory complex I transmembrane arm
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.2 mg/ml
BufferpH: 7.4
Vitrification
Cryogen NameETHANE
Humidity100
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose1.25 e/A**2
Illumination ModeOTHER
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Camera
DetectorFEI FALCON II (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRELION
Resolution By Author3.7 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections167761
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-6772-v19.xml (5.3 KB)
emd-6772-v20.xml (11.2 KB)
emd-6772.xml (5.3 KB)
Map dataemd_6772.map.gz (22.8 MB)
Imagesemd_6772.png (20.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-6772
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 6.3 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 6.4 MB
Session file for UCSF-Chimera, 26.9 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 6.5 MB
Session file for UCSF-Chimera, 4 MB