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- EMDB-3905: Cryo-EM density map of the human MHC-I peptide loading complex -

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Basic information

Entry
Database: EMDB / ID: 3905
TitleCryo-EM density map of the human MHC-I peptide loading complex
SampleProtein Complex
SourceHomo sapiens / human
Map dataCryo-EM structure of protein complex
Methodsingle particle reconstruction, at 9.9 Å resolution
AuthorsJanuliene D / Blees A / Trowitzsch S / Tampe R / Moeller A
CitationNature, 2017

Nature, 2017 Yorodumi Papers
Structure of the human MHC-I peptide-loading complex.
Andreas Blees / Dovile Januliene / Tommy Hofmann / Nicole Koller / Carla Schmidt / Simon Trowitzsch / Arne Moeller / Robert Tampé

DateDeposition: Oct 7, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 15, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3905.map.gz (map file in CCP4 format, 199345 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
368 pix
1.08 Å/pix.
= 396.336 Å
368 pix
1.08 Å/pix.
= 396.336 Å
368 pix
1.08 Å/pix.
= 396.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.077 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.011932677 - 0.056267243
Average (Standard dev.)0.0006212709 (0.003730394)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions368368368
Origin000
Limit367367367
Spacing368368368
CellA=B=C: 396.336 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0771.0771.077
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z396.336396.336396.336
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0120.0560.001

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Supplemental data

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Sample components

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Entire Protein Complex

EntireName: Protein Complex / Number of components: 1
MassExperimental: 650 kDa

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Component #1: protein, Protein Complex

ProteinName: Protein Complex / Recombinant expression: No
MassExperimental: 650 kDa
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / 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: 55 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53666
3D reconstructionSoftware: RELION
CTF correction: CTF correction was performed internally in Relion
Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • 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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