5U1D

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the transporter associated with antigen processing trapped by herpes simplex virus.

Oldham, M.L.Grigorieff, N.Chen, J.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.21829
  • Primary Citation of Related Structures:  
    5U1D

  • PubMed 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 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.


  • Organizational Affiliation

    Howard Hughes Medical Institute, The Rockefeller University, New York, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen peptide transporter 1748Homo sapiensMutation(s): 0 
Gene Names: TAP1ABCB2PSF1RING4Y3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03518 (Homo sapiens)
Explore Q03518 
Go to UniProtKB:  Q03518
PHAROS:  Q03518
GTEx:  ENSG00000168394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03518
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen peptide transporter 2686Homo sapiensMutation(s): 0 
Gene Names: TAP2ABCB3PSF2RING11Y1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03519 (Homo sapiens)
Explore Q03519 
Go to UniProtKB:  Q03519
PHAROS:  Q03519
GTEx:  ENSG00000204267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03519
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TAP transporter inhibitor ICP47C [auth X]88Human alphaherpesvirus 1Mutation(s): 0 
Gene Names: US12
UniProt
Find proteins for A0A140GKJ0 (Human herpesvirus 1)
Explore A0A140GKJ0 
Go to UniProtKB:  A0A140GKJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140GKJ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.09
MODEL REFINEMENTREFMACccp4-7.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references