[English] 日本語
- EMDB-6776: Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 6776
TitleCryo-EM architecture of human respiratory chain megacomplex-I2III2IV2
SampleHuman respiratory chain megacomplex-I2III2IV2
SourceHomo sapiens / human
Map data
Methodsingle particle reconstruction, at 17.4 Å resolution
AuthorsGu J / Wu M / Yang M
CitationCell, 2017, 170, 1247-1257.e12

Cell, 2017, 170, 1247-1257.e12 StrPapers
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2.
Runyu Guo / Shuai Zong / Meng Wu / Jinke Gu / Maojun Yang

Validation ReportPDB-ID: 5xti

SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xti
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_6776.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.083 Å
Contour Level:0.0056 (by author), 0.0056 (movie #1):
Minimum - Maximum-0.029248776 - 0.054389697
Average (Standard dev.)0.00030900445 (0.005835759)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0290.0540.000

Supplemental data

Sample components

Entire Human respiratory chain megacomplex-I2III2IV2

EntireName: Human respiratory chain megacomplex-I2III2IV2 / Number of components: 1
MassExperimental: 2.9 MDa

Component #1: protein, Human respiratory chain megacomplex-I2III2IV2

ProteinName: Human respiratory chain megacomplex-I2III2IV2 / Recombinant expression: No
MassExperimental: 2.9 MDa
SourceSpecies: Homo sapiens / human

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 8600
3D reconstructionSoftware: RELION / Resolution: 17.4 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

About Yorodumi


Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more