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- EMDB-8482: Cryo-EM structure of the human TAP ATP-Binding Cassette Transporter -

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Basic information

Entry
Database: EMDB / ID: 8482
TitleCryo-EM structure of the human TAP ATP-Binding Cassette Transporter
SampleTAP ATP-Binding Cassette Transporter
SourceHomo sapiens / human
Map dataHuman TAP ATP-Binding Cassette Transporter, full map from Frealign alignment, scaled to molecule, B-factor corrected to -150 Angstrom^2, and moved into new padded unit cell
Methodsingle particle reconstruction, at 3.97 Å resolution
AuthorsOldham ML / Chen J
CitationElife, 2016, 5

Elife, 2016, 5 StrPapers
Structure of the transporter associated with antigen processing trapped by herpes simplex virus.
Michael L Oldham / Nikolaus Grigorieff / Jue Chen

DateDeposition: Nov 28, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Nov 28, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5u1d
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8482.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

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AxesY (Sec.)X (Row.)Z (Col.)
256 pix
0.45 Å/pix.
= 115.999 Å
256 pix
0.36 Å/pix.
= 92.5 Å
256 pix
0.45 Å/pix.
= 115.999 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX: 0.36133 Å / Y: 0.45312 Å / Z: 0.45312 Å
Density
Contour Level:0.6 (by emdb), 0.6 (movie #1):
Minimum - Maximum-2.1199465 - 2.8055391
Average (Standard dev.)0.03569515 (0.2523155)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA: 92.50048 Å / B: 115.99872 Å / C: 115.99872 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z0.3613281250.453121093750.45312109375
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z92.500115.999115.999
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.1202.8060.036

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Supplemental data

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Sample components

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Entire TAP ATP-Binding Cassette Transporter

EntireName: TAP ATP-Binding Cassette Transporter / Number of components: 4

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Component #1: protein, TAP ATP-Binding Cassette Transporter

ProteinName: TAP ATP-Binding Cassette Transporter / Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Komagataella pastoris / fungus / Vector: pPICZa

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Component #2: protein, Antigen peptide transporter 1

ProteinName: Antigen peptide transporter 1 / Recombinant expression: No
MassTheoretical: 81.034289 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #3: protein, Antigen peptide transporter 2

ProteinName: Antigen peptide transporter 2 / Recombinant expression: No
MassTheoretical: 75.736508 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #4: protein, TAP transporter inhibitor ICP47

ProteinName: TAP transporter inhibitor ICP47 / Recombinant expression: No
MassTheoretical: 9.850086 kDa
Source (engineered)Expression System: Human herpesvirus 1 / virus / ヒトヘルペスウイルス 1

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 22 K / Humidity: 95 %

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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: 1.48 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 0.01 mm / Imaging mode: BRIGHT FIELD / Energy filter: Gatan Image Filter (GIF)
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 100 - 100 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3875

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 501973
3D reconstructionSoftware: Frealign / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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