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

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Basic information

Database: EMDB / ID: 3905
TitleCryo-EM density map of the human MHC-I peptide loading complex
Map dataCryo-EM structure of protein complex
SampleProtein Complex:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 9.9 Å resolution
AuthorsJanuliene D / Blees A / Trowitzsch S / Tampe R / Moeller A
CitationJournal: Nature / Year: 2017
Title: Structure of the human MHC-I peptide-loading complex.
Authors: 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 28, 2018

Structure visualization

  • 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
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 396.336 Å
α=β=γ: 90.0 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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0120.0560.001

Supplemental data

Sample components

Entire Protein Complex

EntireName: Protein Complex / Number of components: 1

Component #1: protein, Protein Complex

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

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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)

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 estimation)

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