1A1N | pdb_00001a1n

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

• PDB DOI: https://doi.org/10.2210/pdb1A1N/pdb

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


• 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: 2.00 Å
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/s1074-7613(00)80429-x
• Primary Citation Related Structures: 
  1A1N


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.69 kDa 
• Atom Count: 3,511 
• Modeled Residue Count: 383 
• Deposited Residue Count: 383 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, BW-53 B*5301 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: T7
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	99	Homo sapiens	Mutation(s): 0  Gene Names: T7
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
PEPTIDE VPLRPMTY	C	8	Human immunodeficiency virus 1	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50	α = 90
b = 80.5	β = 90
c = 105.9	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary