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- EMDB-6776: Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2 -

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Basic information

Entry
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 Yorodumi Papers
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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5xti
  • Surface level: 0.0056
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

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

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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 package.

Voxel sizeX=Y=Z: 1.083 Å
Density
Contour Level:0.0056 (by author), 0.0056 (movie #1):
Minimum - Maximum-0.029248776 - 0.054389697
Average (Standard dev.)0.00030900445 (0.005835759)
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-0.0290.0540.000

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Supplemental data

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Sample components

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Entire Human respiratory chain megacomplex-I2III2IV2

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

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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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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: 8600
3D reconstructionSoftware: RELION / Resolution: 17.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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