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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: EMD-8482
TitleCryo-EM structure of the human TAP ATP-Binding Cassette Transporter
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
Sample
  • Complex: TAP ATP-Binding Cassette Transporter
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: TAP transporter inhibitor ICP47
Keywordsmembrane / protein / ABC transporter / antigen / presentation / TRANSPORT PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / ABC-type peptide transporter activity / TAP1 binding / TAP2 binding / peptide antigen transport ...symbiont-mediated suppression of host antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent / tapasin binding / ABC-type antigen peptide transporter / ABC-type peptide antigen transporter activity / TAP complex / ABC-type peptide transporter activity / TAP1 binding / TAP2 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transmembrane transporter activity / peptide transport / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / centriolar satellite / endoplasmic reticulum-Golgi intermediate compartment membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ADP binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / transmembrane transport / antigen processing and presentation of endogenous peptide antigen via MHC class I / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / protein transport / ER-Phagosome pathway / host cell cytoplasm / adaptive immune response / nuclear speck / virus-mediated perturbation of host defense response / endoplasmic reticulum membrane / host cell nucleus / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Herpesvirus ICP47 / Herpesvirus US12 family / Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site ...Herpesvirus ICP47 / Herpesvirus US12 family / Antigen peptide transporter 2 / ABC transporter Tap-like / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ICP47 protein / Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Human herpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsOldham ML / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2016
Title: Structure of the transporter associated with antigen processing trapped by herpes simplex virus.
Authors: Michael L Oldham / Nikolaus Grigorieff / Jue Chen /
Abstract: The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved ...The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process.
History
DepositionNov 28, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseJan 11, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8482.png

Downloads & links

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Map

FileDownload / File: emd_8482.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.45 Å/pix.
x 256 pix.
= 115.999 Å		0.36 Å/pix.
x 256 pix.
= 92.5 Å		0.45 Å/pix.
x 256 pix.
= 115.999 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX: 0.36133 Å / Y: 0.45312 Å / Z: 0.45312 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.6 / Movie #1: 0.6
Minimum - Maximum-2.1199465 - 2.8055391
Average (Standard dev.)0.03569515 (±0.2523155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions256256256
Spacing256256256
CellA: 92.50048 Å / B: 115.99872 Å / C: 115.99872 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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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Additional map: Human TAP ATP-Binding Cassette Transporter, half map 2...

Fileemd_8482_additional_1.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, half map 2 from Frealign alignment before move to new unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human TAP ATP-Binding Cassette Transporter, half map 1...

Fileemd_8482_additional_2.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, half map 1 from Frealign alignment before move to new unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human TAP ATP-Binding Cassette Transporter, full map 1...

Fileemd_8482_additional_3.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, full map 1 from Frealign alignment, scaled to molecule, and moved into new padded unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human TAP ATP-Binding Cassette Transporter, full map from...

Fileemd_8482_additional_4.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, full map from Frealign alignment before moving to new unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human TAP ATP-Binding Cassette Transporter, half map 2...

Fileemd_8482_additional_5.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, half map 2 from Frealign alignment, scaled to molecule, and moved into new padded unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human TAP ATP-Binding Cassette Transporter, half map 1...

Fileemd_8482_additional_6.map
AnnotationHuman TAP ATP-Binding Cassette Transporter, half map 1 from Frealign alignment, scaled to molecule, and moved into new padded unit cell
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TAP ATP-Binding Cassette Transporter

EntireName: TAP ATP-Binding Cassette Transporter
Components
  • Complex: TAP ATP-Binding Cassette Transporter
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: TAP transporter inhibitor ICP47

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Supramolecule #1: TAP ATP-Binding Cassette Transporter

SupramoleculeName: TAP ATP-Binding Cassette Transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antigen peptide transporter 1

MacromoleculeName: Antigen peptide transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.034289 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG ...String:
MASSRCPAPR GCRCLPGASL AWLGTVLLLL ADWVLLRTAL PRIFSLLVPT ALPLLRVWAV GLSRWAVLWL GACGVLRATV GSKSENAGA QGWLAALKPL AAALGLALPG LALFRELISW GAPGSADSTR LLHWGSHPTA FVVSYAAALP AAALWHKLGS L WVPGGQGG SGNPVRRLLG CLGSETRRLS LFLVLVVLSS LGEMAIPFFT GRLTDWILQD GSADTFTRNL TLMSILTIAS AV LEFVGDG IYNNTMGHVH SHLQGEVFGA VLRQETEFFQ QNQTGNIMSR VTEDTSTLSD SLSENLSLFL WYLVRGLCLL GIM LWGSVS LTMVTLITLP LLFLLPKKVG KWYQLLEVQV RESLAKSSQV AIEALSAMPT VRSFANEEGE AQKFREKLQE IKTL NQKEA VAYAVNSWTT SISGMLLKVG ILYIGGQLVT SGAVSSGNLV TFVLYQMQFT QAVEVLLSIY PRVQKAVGSS EKIFE YLDR TPRCPPSGLL TPLHLEGLVQ FQDVSFAYPN RPDVLVLQGL TFTLRPGEVT ALVGPNGSGK STVAALLQNL YQPTGG QLL LDGKPLPQYE HRYLHRQVAA VGQEPQVFGR SLQENIAYGL TQKPTMEEIT AAAVKSGAHS FISGLPQGYD TEVDEAG SQ LSGGQRQAVA LARALIRKPC VLILDDATSA LDANSQLQVE QLLYESPERY SRSVLLITQH LSLVEQADHI LFLEGGAI R EGGTHQQLME KKGCYWAMVQ APADAPE

UniProtKB: Antigen peptide transporter 1

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Macromolecule #2: Antigen peptide transporter 2

MacromoleculeName: Antigen peptide transporter 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.736508 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MRLPDLRPWT SLLLVDAALL WLLQGPLGTL LPQGLPGLWL EGTLRLGGLW GLLKLRGLLG FVGTLLLPLC LATPLTVSLR ALVAGASRA PPARVASAPW SWLLVGYGAA GLSWSLWAVL SPPGAQEKEQ DQVNNKVLMW RLLKLSRPDL PLLVAAFFFL V LAVLGETL ...String:
MRLPDLRPWT SLLLVDAALL WLLQGPLGTL LPQGLPGLWL EGTLRLGGLW GLLKLRGLLG FVGTLLLPLC LATPLTVSLR ALVAGASRA PPARVASAPW SWLLVGYGAA GLSWSLWAVL SPPGAQEKEQ DQVNNKVLMW RLLKLSRPDL PLLVAAFFFL V LAVLGETL IPHYSGRVID ILGGDFDPHA FASAIFFMCL FSFGSSLSAG CRGGCFTYTM SRINLRIREQ LFSSLLRQDL GF FQETKTG ELNSRLSSDT TLMSNWLPLN ANVLLRSLVK VVGLYGFMLS ISPRLTLLSL LHMPFTIAAE KVYNTRHQEV LRE IQDAVA RAGQVVREAV GGLQTVRSFG AEEHEVCRYK EALEQCRQLY WRRDLERALY LLVRRVLHLG VQMLMLSCGL QQMQ DGELT QGSLLSFMIY QESVGSYVQT LVYIYGDMLS NVGAAEKVFS YMDRQPNLPS PGTLAPTTLQ GVVKFQDVSF AYPNR PDRP VLKGLTFTLR PGEVTALVGP NGSGKSTVAA LLQNLYQPTG GQVLLDEKPI SQYEHCYLHS QVVSVGQEPV LFSGSV RNN IAYGLQSCED DKVMAAAQAA HADDFIQEME HGIYTDVGEK GSQLAAGQKQ RLAIARALVR DPRVLILDEA TSALDVQ CE QALQDWNSRG DRTVLVIAHR LQTVQRAHQI LVLQEGKLQK LAQL

UniProtKB: Antigen peptide transporter 2

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Macromolecule #3: TAP transporter inhibitor ICP47

MacromoleculeName: TAP transporter inhibitor ICP47 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1)
Molecular weightTheoretical: 9.850086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSWALEMADT FLDNMRVGPR TYADVRDEIN KRGREDREAA RTAVHDPERP LLRSPGLLPE IAPNASLGVV HRRTGGTVTD SPRNPVTR

UniProtKB: ICP47 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
2.0 mMTCEP
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Name: GIF
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 3875 / Average exposure time: 0.2 sec. / Average electron dose: 1.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 501973
Startup modelType of model: EMDB MAP
EMDB ID:

6533

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.09) / Number images used: 501973
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 150 / Target criteria: R factor and FSC
Output model

PDB-5u1d:
Cryo-EM structure of the human TAP ATP-Binding Cassette Transporter

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