4E5X | pdb_00004e5x

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2396
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Groups
UniProt Group	P0C213
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68979
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.241 (Depositor), 0.241 (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

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Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Li, L.

Bouvier, M.

Revision History (Full details and data files)

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