4E5X

Crystal structure of a complex between the human adenovirus type 2 E3-19K protein and MHC class I molecule HLA-A2/Tax

• PDB DOI: https://doi.org/10.2210/pdb4E5X/pdb

• Classification: IMMUNE SYSTEM/TRANSCRIPTION
• Organism(s): Homo sapiens, Human T-cell lymphotropic virus type 1 (african isolate), Human adenovirus 6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-14 Released: 2012-10-10 
• Deposition Author(s): Li, L., Bouvier, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of adenovirus E3-19K bound to HLA-A2 reveals mechanism for immunomodulation.

Li, L., Muzahim, Y., Bouvier, M.

(2012) Nat Struct Mol Biol 19: 1176-1181

• PubMed: 23042604 
• DOI: https://doi.org/10.1038/nsmb.2396
• Primary Citation of Related Structures:  
  4E5X


• PubMed Abstract: 
  

  E3-19K binds to and retains MHC class I molecules in the endoplasmic reticulum, suppressing anti-adenovirus activities of T cells. We determined the structure of the adenovirus serotype 2 (Ad2, species C) E3-19K-HLA-A2 complex to 1.95-Å resolution. Ad2 E3-19K binds to the N terminus of the HLA-A2 groove, contacting the α1, α2 and α3 domains and β(2)m. Ad2 E3-19K has a unique structure comprising a large N-terminal domain, formed by two partially overlapping β-sheets arranged in a V shape, and a C-terminal α-helix and tail. The structure reveals determinants in E3-19K and HLA-A2 that are important for complex formation; conservation of some of these determinants in E3-19K proteins of different species and MHC I molecules of different loci suggests a universal binding mode for all E3-19K proteins. Our structure is important for understanding the immunomodulatory function of E3-19K.

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Organizational Affiliation: 

Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.49 kDa 
• Atom Count: 8,439 
• Modelled Residue Count: 964 
• Deposited Residue Count: 968 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, Beta-2-M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Tax-1	C, F	9	Human T-cell lymphotropic virus type 1 (african isolate)	Mutation(s): 0
UniProt
Find proteins for P0C213 (Human T-cell leukemia virus 1 (isolate Zaire EL subtype B)) Explore P0C213  Go to UniProtKB:  P0C213

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Early E3 18.5 kDa glycoprotein	G, H	100	Human adenovirus 6	Mutation(s): 0
UniProt
Find proteins for P68979 (Human adenovirus C serotype 6) Explore P68979  Go to UniProtKB:  P68979

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.19	α = 90
b = 133.67	β = 90
c = 196.72	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Li, L., Bouvier, M.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary