Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 44.96 kDa 
• Atom Count: 3683 
• Residue Count: 385 
• Unique protein chains: 3

2BVO

Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs Potentially Associated with Long-Term Non-Progression

• DOI: 10.2210/pdb2BVO/pdb

• Classification: GLYCOPROTEIN/PEPTIDE
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-07-01 Released: 2005-09-13 
• Deposition Author(s): Stewart-Jones, G.B., Gillespie, G., Overton, I.M., Kaul, R., Roche, P., Mcmichael, A.J., Rowland-Jones, S., Jones, E.Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression.

Stewart-Jones, G.B., Gillespie, G., Overton, I.M., Kaul, R., Roche, P., McMichael, A.J., Rowland-Jones, S., Jones, E.Y.

(2005) J Immunol 175: 2459-2468

• PubMed: 16081817 
• DOI: 10.4049/jimmunol.175.4.2459
• Primary Citation of Related Structures:  
  2BVQ, 2BVP, 2BVO


• PubMed Abstract: 
  

Long-term nonprogression during acute HIV infection has been strongly associated with HLA-B*5701 or HLA-B*5703. In this study, we present the high resolution crystal structures of HLA-B*5703 complexes with three HIV-1 epitopes: ISPRTLNAW (ISP), KAFSPEVIPMF (KAF-11), and KAFSPEVI (KAF-8). These reveal peptide anchoring at position 2 and their C termini. The different peptide lengths and primary sequences are accommodated by variation in the specific contacts made to the HLA-B*5703, flexibility in water structure, and conformational adjustment of side chains within the peptide-binding groove. The peptides adopt markedly different conformations, and trap variable numbers of water molecules, near a cluster of tyrosine side chains located in the central region of the peptide-binding groove. The KAF-11 epitope completely encompasses the shorter KAF-8 epitope but the peptides are presented in different conformations; the KAF-11 peptide arches out of the peptide-binding groove, exposing a significant main chain surface area. Bioinformatic analysis of the MHC side chains observed to contribute to the peptide anchor specificity, and other specific peptide contacts, reveals HLA alleles associated with long-term nonprogression and a number of related HLA alleles that may share overlapping peptide repertoires with HLA-B*5703 and thus may display a similar capacity for efficient immune control of HIV-1 infection.

---

Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889 GTEx  ENSG00000234745

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GAG PROTEIN	C	11	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
Find proteins for Q70A61 (Human immunodeficiency virus 1) Explore Q70A61  Go to UniProtKB:  Q70A61

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.235 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.589	α = 90
b = 81.769	β = 90
c = 110.137	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-01 
• Released Date: 2005-09-13 
Deposition Author(s): Stewart-Jones, G.B., Gillespie, G., Overton, I.M., Kaul, R., Roche, P., Mcmichael, A.J., Rowland-Jones, S., Jones, E.Y.

Revision History 

• Version 1.0: 2005-09-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references, Other