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- EMDB-70314: Transporter associated with antigen processing (TAP) bound to the... -

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Basic information

Entry
Database: EMDB / ID: EMD-70314
TitleTransporter associated with antigen processing (TAP) bound to the viral protein BNLF2a in the inward-facing state
Map dataUnsharpened map
Sample
  • Complex: Ternary complex of the heterodimer TAP1 and TAP2 bound to the viral inhibitor BNLF2a
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: TAP transport inhibitor BNLF2a
KeywordsABC transporter / antigen processing / peptide transporter / MEMBRANE PROTEIN / immune evasion / Epstein-Barr / herpesvirus
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 peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / TAP2 binding / TAP1 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 peptide antigen transporter activity / ABC-type antigen peptide transporter / TAP complex / ABC-type peptide transporter activity / TAP2 binding / TAP1 binding / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / endoplasmic reticulum-Golgi intermediate compartment membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / defense response / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / transmembrane transport / centriolar satellite / phagocytic vesicle membrane / protein transport / ER-Phagosome pathway / adaptive immune response / nuclear speck / host cell endoplasmic reticulum membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
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 ...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
Protein BNLF2a / Antigen peptide transporter 1 / Antigen peptide transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human) / human gammaherpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLee J / Manon V / Chen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007739 United States
CitationJournal: To Be Published
Title: Transporter associated with antigen processing (TAP) bound to the viral protein BNLF2a in the inward-facing state
Authors: Lee J / Manon V / Chen J
History
DepositionApr 24, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70314.png

Downloads & links

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Map

FileDownload / File: emd_70314.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.35883906 - 0.85937667
Average (Standard dev.)0.00022533868 (±0.021778813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_70314_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70314_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70314_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of the heterodimer TAP1 and TAP2 bound to the vir...

EntireName: Ternary complex of the heterodimer TAP1 and TAP2 bound to the viral inhibitor BNLF2a
Components
  • Complex: Ternary complex of the heterodimer TAP1 and TAP2 bound to the viral inhibitor BNLF2a
    • Protein or peptide: Antigen peptide transporter 2
    • Protein or peptide: Antigen peptide transporter 1
    • Protein or peptide: TAP transport inhibitor BNLF2a

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Supramolecule #1: Ternary complex of the heterodimer TAP1 and TAP2 bound to the vir...

SupramoleculeName: Ternary complex of the heterodimer TAP1 and TAP2 bound to the viral inhibitor BNLF2a
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Details: TAP1 is C-terminally tagged with Spycatcher and BNLF2a is N-terminally tagged with GFP and Spytag
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 182 KDa

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Macromolecule #1: Antigen peptide transporter 2

MacromoleculeName: Antigen peptide transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.736508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 #2: TAP transport inhibitor BNLF2a

MacromoleculeName: TAP transport inhibitor BNLF2a / type: protein_or_peptide / ID: 2
Details: N-terminally fused to a GFP, Precission protease site, and Spytag. The GFP is cleaved during purification.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 9.823499 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GPTAAAAMGR GVPHIVMVDA YKRYKGGGSG GSGGGMVHVL ERALLEQQSS ACGLPGSSTE TRPSHPCPED PDVSRLRLLL VVLCVLFGL LCLLLI

UniProtKB: Protein BNLF2a

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Macromolecule #3: Antigen peptide transporter 1

MacromoleculeName: Antigen peptide transporter 1 / type: protein_or_peptide / ID: 3
Details: C-terminally fused to a TEV protease cut site and Spycatcher
Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type antigen peptide transporter
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.839172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 APADAPESAQ LEGSGGGAMV TTLSGLSGEQ GPSGDMTTEE DSATHIKFSK RDEDGRELA GATMELRDSS GKTISTWISD GHVKDFYLYP GKYTFVETAA PDGYEVATPI EFTVNEDGQV TVDGEATEGD AHTSGGGHHH HHHHHHH

UniProtKB: Antigen peptide transporter 1

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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

Concentration6 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
50.0 mMHEPES2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid
200.0 mMKClpotassium chloride
1.0 mMDTTdithiothreitol
0.004 %GDNglyco-diosgenin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
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: 3395985
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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