Biological Assembly 1  

 3D View: Structure

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

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

Macromolecule Content

• Total Structure Weight: 44691.64 
• Atom Count: 3153 
• Residue Count: 383 
• Unique protein chains: 3

1A1N

MHC CLASS I MOLECULE B*3501 COMPLEXED WITH PEPTIDE VPLRPMTY FROM THE NEF PROTEIN (75-82) OF HIV1

• DOI: 10.2210/pdb1A1N/pdb

• Classification: COMPLEX (ANTIGEN/PEPTIDE)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 1997-12-11 Released: 1998-04-08 
• Deposition Author(s): Smith, K.J., Reid, S.W., Stuart, D.I., Mcmichael, A.J., Jones, E.Y., Bell, J.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.203 

Literature

An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501.

Smith, K.J., Reid, S.W., Stuart, D.I., McMichael, A.J., Jones, E.Y., Bell, J.I.

(1996) Immunity 4: 203-213

• PubMed: 8624811 


• PubMed Abstract: 
  

The crystal structure of the human major histocompatibility complex class I B allele HLA B*3501 complexed with the 8-mer peptide epitope HIV1 Nef 75-82 (VPLRPMTY) has been determined at 2.0 angstrom resolution. Comparison with the crystal structure of the closely related allele HLA B*5301 reveals the structural basis for the tyrosine specificity of the B*3501 F pocket. The structure also reveals a novel conformation of the 8-mer peptide within the binding groove. The positions of the peptide N and C termini are nonstandard, but the classic pattern of hydrogen bonding to nonpolymorphic MHC class I residues is maintained, at the N terminus by addition of a water molecule, and at the C terminus by a substantial shift in the alpha 2 helix.

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Organizational Affiliation: 

Nuffield Department of Clinical Medicine, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, BW-53 B*5301 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B (HLAB)
Find proteins for P30685 (Homo sapiens) Go to Gene View: HLA-B Go to UniProtKB:  P30685

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PEPTIDE VPLRPMTY	C	8	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.000	α = 90.00
b = 80.500	β = 90.00
c = 105.900	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-12-11 
• Released Date: 1998-04-08 
• Deposition Author(s): Smith, K.J., Reid, S.W., Stuart, D.I., Mcmichael, A.J., Jones, E.Y., Bell, J.I.

Revision History 

• Version 1.0: 1998-04-08
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance