5U1D

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

• PDB DOI:  https://doi.org/10.2210/pdb5U1D/pdb
• EM Map EMD-8482: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Human alphaherpesvirus 1
• Expression System: Komagataella pastoris, Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-11-28 Released: 2017-01-11 
• Deposition Author(s): Oldham, M.L., Chen, J., Grigorieff, N.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

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

Literature

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

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

(2016) Elife 5

• PubMed: 27935481 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 166.62 kDa 
• Atom Count: 7,815 
• Modelled Residue Count: 1,168 
• Deposited Residue Count: 1,522 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen peptide transporter 1	A	748	Homo sapiens	Mutation(s): 0  Gene Names: TAP1, ABCB2, PSF1, RING4, Y3 EC: 7.4.2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q03518 (Homo sapiens) Explore Q03518  Go to UniProtKB:  Q03518
PHAROS:  Q03518

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen peptide transporter 2	B	686	Homo sapiens	Mutation(s): 0  Gene Names: TAP2, ABCB3, PSF2, RING11, Y1 EC: 7.4.2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q03519 (Homo sapiens) Explore Q03519  Go to UniProtKB:  Q03519
PHAROS:  Q03519

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TAP transporter inhibitor ICP47	C [auth X]	88	Human alphaherpesvirus 1	Mutation(s): 0  Gene Names: US12
UniProt
Find proteins for A0A140GKJ0 (Human herpesvirus 1) Explore A0A140GKJ0  Go to UniProtKB:  A0A140GKJ0

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN	9.09
MODEL REFINEMENT	REFMAC	ccp4-7.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Oldham, M.L., Chen, J., Grigorieff, N.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• 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