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- PDB-9oci: Transporter associated with antigen processing (TAP) bound to the... -

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Basic information

Entry
Database: PDB / ID: 9oci
TitleTransporter associated with antigen processing (TAP) bound to the viral protein rhUS6 in the outward-facing open state
Components
  • (Antigen peptide transporter ...) x 2
  • TAP transport inhibitor rhUS6
KeywordsMEMBRANE PROTEIN / ABC transporter / antigen processing / peptide transporter / immune evasion / cytomegalovirus / herpesvirus
Function / homology
Function and homology information


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 / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / TAP2 binding ...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 / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / TAP2 binding / TAP1 binding / peptide transport / peptide transmembrane transporter activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / MHC class I protein binding / endoplasmic reticulum-Golgi intermediate compartment membrane / T cell mediated cytotoxicity / 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 / defense response / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / ADP binding / positive regulation of T cell mediated cytotoxicity / transmembrane transport / peptide antigen binding / phagocytic vesicle membrane / centriolar satellite / protein transport / ER-Phagosome pathway / adaptive immune response / nuclear speck / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Antigen peptide transporter 1 / Antigen peptide transporter 2 / Rh185
Similarity search - Component
Biological speciesHomo sapiens (human)
macacine betaherpesvirus 3 (Rhesus cytomegalovirus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLee, J. / Manon, V. / Chen, J.
Funding support United States, 2items
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: Proc Natl Acad Sci U S A / Year: 2025
Title: Structurally diverse viral inhibitors converge on a shared mechanism to stall the antigen transporter TAP.
Authors: James Lee / Victor Manon / Jue Chen /
Abstract: In the host-pathogen arms race, herpesviruses and poxviruses encode proteins that sabotage the transporter associated with antigen processing (TAP), thereby suppressing MHC-I antigen presentation and ...In the host-pathogen arms race, herpesviruses and poxviruses encode proteins that sabotage the transporter associated with antigen processing (TAP), thereby suppressing MHC-I antigen presentation and enabling lifelong infection. Of the five known viral TAP inhibitors, only the herpes simplex virus (HSV) protein ICP47 has been structurally resolved. We now report cryoelectron microscopy structures of TAP in complex with the remaining four: BNLF2a (Epstein-Barr virus), hUS6 (human cytomegalovirus), bUL49.5 (bovine herpesvirus 1), and CPXV012 (cowpox virus), assembling a structural atlas of viral TAP evasion. Despite employing divergent sequences, folds, and conformational targets, these viral inhibitors converge on a common strategy: they stall TAP from the alternating access cycle, precluding peptide entry into the ER and shielding infected cells from cytotoxic T cell surveillance. These findings reveal striking functional convergence and provide a structural framework for rational antiviral design.
History
DepositionApr 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Antigen peptide transporter 2
D: TAP transport inhibitor rhUS6
A: Antigen peptide transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,9737
Polymers195,9903
Non-polymers9834
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antigen peptide transporter ... , 2 types, 2 molecules BA

#1: Protein Antigen peptide transporter 2 / APT2 / ATP-binding cassette sub-family B member 3 / Peptide supply factor 2 / Peptide transporter ...APT2 / ATP-binding cassette sub-family B member 3 / Peptide supply factor 2 / Peptide transporter PSF2 / PSF-2 / Peptide transporter TAP2 / Peptide transporter involved in antigen processing 2 / Really interesting new gene 11 protein


Mass: 75736.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAP2, ABCB3, PSF2, RING11, Y1 / Production host: Homo sapiens (human) / Strain (production host): HEK293 GnTI- / References: UniProt: Q03519
#3: Protein Antigen peptide transporter 1 / APT1 / ATP-binding cassette sub-family B member 2 / Peptide supply factor 1 / Peptide transporter ...APT1 / ATP-binding cassette sub-family B member 2 / Peptide supply factor 1 / Peptide transporter PSF1 / PSF-1 / Peptide transporter TAP1 / Peptide transporter involved in antigen processing 1 / Really interesting new gene 4 protein / RING4


Mass: 95839.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminally fused to a TEV protease cut site and Spycatcher
Source: (gene. exp.) Homo sapiens (human) / Gene: TAP1, ABCB2, PSF1, RING4, Y3 / Production host: Homo sapiens (human)
References: UniProt: Q03518, ABC-type antigen peptide transporter

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Protein , 1 types, 1 molecules D

#2: Protein TAP transport inhibitor rhUS6


Mass: 24414.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminally fused to a TEV protease cut site, Spytag, a Precission protease site, and eGFP.
Source: (gene. exp.) macacine betaherpesvirus 3 (Rhesus cytomegalovirus)
Production host: Homo sapiens (human) / Strain (production host): HEK293 GnTI- / References: UniProt: Q2FAB2

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of the heterodimer TAP1 and TAP2 bound to the viral inhibitor Rh185
Type: COMPLEX
Details: TAP1 is C-terminally tagged with Spycatcher and Rh185 is C-terminally tagged with GFP and Spytag
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.196 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293S GnTI-
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2200 mMpotassium chlorideKCl1
31 mMdithiothreitolDTT1
40.004 %glyco-diosgeninGDN1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.8.3particle selection
2SerialEM3.7image acquisition
4CTFFINDCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3395985
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46902 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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