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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
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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.
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