Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 44.61 kDa 
• Atom Count: 3363 
• Residue Count: 383 
• Unique protein chains: 3

3RL2

HIV Nef derived peptide Nef73 complexed to HLA-A*0301

• DOI: 10.2210/pdb3RL2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-19 Released: 2012-02-29 
• Deposition Author(s): Zhang, S., Liu, J., Cheng, H., Tan, S., Qi, J., Yan, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Literature

Structural basis of cross-allele presentation by HLA-A*0301 and HLA-A*1101 revealed by two HIV-derived peptide complexes

Zhang, S., Liu, J., Cheng, H., Tan, S., Qi, J., Yan, J., Gao, G.F.

(2011) Mol Immunol 49: 395-401

• PubMed: 21943705 
• DOI: 10.1016/j.molimm.2011.08.015
• Primary Citation of Related Structures:  
  3RL1, 3RL2


• PubMed Abstract: 
  

Human leukocyte antigens (HLA) are initially classified by serotyping but recently can be re-grouped by their peptide-presentation characteristics into supertypes. Both HLA-A*0301 and HLA-A*1101 are grouped into A3 supertype. Although a number of cross-presented T cell epitopes of HLA-A*0301 and HLA-A*1101 have been identified, the molecular mechanisms of cross-presentation remain elusive. Herein, the structures of HLA-A*0301 with two HIV-derived immunodominant T cell epitopes were solved and their characteristics in comparison with HLA-A*1101 presenting the same peptides were analyzed. The comparable structures of HLA-A*0301 and HLA-A*1101 with subtle differences illustrate the common modes of cross-presented peptides and the strict HLA-restriction of T cell receptor (TCR)-recognition.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-3 alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLAA, HLA-A
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	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
Nef73 peptide from Protein Nef	C	10	Human immunodeficiency virus 1	Mutation(s): 0
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04601  Go to UniProtKB:  P04601

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.054	α = 90
b = 77.424	β = 90
c = 78.707	γ = 90

Software Package:

Software Name	Purpose
DDT	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-19 
• Released Date: 2012-02-29 
Deposition Author(s): Zhang, S., Liu, J., Cheng, H., Tan, S., Qi, J., Yan, J., Gao, G.F.

Revision History 

• Version 1.0: 2012-02-29
  Type: Initial release