PDBsum entry 1a1n

Complex (antigen/peptide)

PDB id: 1a1n

Contents

Protein chains

276 a.a. *

99 a.a. *

Ligands

VAL-PRO-LEU-ARG-PRO-MET-THR-TYR

Waters ×358

* Residue conservation analysis

PDB id:

1a1n

Name:

Complex (antigen/peptide)

Title:

Mhc class i molecule b 3501 Complexed with peptide vplrpmty from the nef protein (75-82) of hiv1

Structure:

Hla class i histocompatibility antigen, bw-53 b 5301 Alpha chain. Chain: a. Synonym: b35. Engineered: yes. Beta-2-microglobulin. Chain: b. Synonym: b35. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Gene: t7. Expressed in: escherichia coli. Expression_system_taxid: 562. Human immunodeficiency virus 1. Organism_taxid: 11676

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.203

Authors:

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

Key ref:

K.J.Smith et al. (1996). An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501. Immunity, 4, 203-213. PubMed id: 8624811 DOI: 10.1016/S1074-7613(00)80429-X

Date:

11-Dec-97 Release date: 08-Apr-98

Protein chain

P01889  (1B07_HUMAN) -  HLA class I histocompatibility antigen, B alpha chain from Homo sapiens

Seq: 362 a.a.

Struc: 276 a.a.*

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 99 a.a.

* PDB and UniProt seqs differ at 23 residue positions (black crosses)

DOI no: 10.1016/S1074-7613(00)80429-X

Immunity 4:203-213 (1996)

PubMed id: 8624811

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

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

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.

Selected figure(s)

Figure 2.
Figure 2. The Structure of the HIV1 Nef Peptide (VPLRPMTY)The views illustrate the peptide viewed through the α2 helix.(A) A 2.0 Å F[o]−F[c] φ[calc] electron density map for which the Nef peptide has been omitted from the phasing model. The electron density is contoured at 2.5 σ and displayed in FRODO ([22]) with the current model for the peptide.(B) A main chain superposition (SHP[39]) of the Nef peptide (light blue) with the peptide main chains from the following structures: HLA-B53/ls6 (red), HLA-B53/HIV2 (purple), H-2K^b/VSV8 (dark blue), HLA-A2/flu (dark green), H-2K^b/SEV9 (yellow), H-2D^b/Flu-np (light green).(C) A superposition of the Nef peptide (green) with the ls6 peptide KPIVQYDNF (red) from the B53/ls6 structure.

Figure 4.
Figure 4. The F Pockets of B3501 and B53Both panels are viewed through the α2 helix and, as in Figure 3, the MHC main chain is represented in green, key side chains are shown in white, dashed lines indicate hydrogen bonds, and light blue spheres mark the positions of tightly bound water molecules.(A) The B3501 F pocket. The polymorphic residue (Gly) at position 83 is not visible from this angle but is solvent exposed and located on a turn of the α1 helix adjacent to residue 82.(B) The B53 F pocket.

The above figures are reprinted by permission from Cell Press: Immunity (1996, 4, 203-213) copyright 1996.

Figures were selected by an automated process.