PDBsum entry: 1a1o

Complex (antigen/peptide)

PDB id: 1a1o

Contents

Protein chains

276 a.a. *

99 a.a. *

Ligands

LYS-PRO-ILE-VAL-GLN-TYR-ASP-ASN-PHE

Waters ×113

* Residue conservation analysis

PDB id:

1a1o

Name:

Complex (antigen/peptide)

Title:

Mhc class i molecule b 5301 Complexed with peptide ls6 (kpivqydnf) from the malaria parasite p. Falciparum

Structure:

Hla class i histocompatibility antigen, bw-53 b 5301 Alpha chain. Chain: a. Synonym: b53. Engineered: yes. Beta-2-microglobulin. Chain: b. Synonym: b53. 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:

2.30Å R-factor: 0.168

Authors:

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

Key ref:

K.J.Smith et al. (1996). Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Immunity, 4, 215-228. PubMed id: 8624812 DOI: 10.1016/S1074-7613(00)80430-6

Date:

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

Protein chain

P30491  (1B53_HUMAN) -  HLA class I histocompatibility antigen, B-53 alpha chain

Seq: 362 a.a.

Struc: 276 a.a.*

Protein chain

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin

Seq: 119 a.a.

Struc: 99 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (8 terms)
• Biological process: immune response (8 terms)
• Biochemical function: protein binding (1 term)

DOI no: 10.1016/S1074-7613(00)80430-6

Immunity 4:215-228 (1996)

PubMed id: 8624812

Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53.

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

ABSTRACT

The structure of the human MHC class I molecule HLA-B53 complexed to two nonameric peptide epitopes (from the malaria parasite P. falciparum and the HIV2 gag protein) has been determined by X-ray crystallography at 2.3 angstrom resolution. The structures reveal the architecture of a Pro-specific B pocket common to many HLA-B alleles. Relative to other alleles, the B53 peptide-binding groove is widened by a significant (up to 1.25 angstrom) shift in the position of the alpha 1 helix. Within this groove, bound water molecules, acting in concert with the side chains of polymorphic residues, provide the functional malleability of the MHC, which enables the high affinity/low specificity binding of multiple peptide epitopes.

Selected figure(s)

Figure 3.
Figure 3. The B53 Peptide-Binding Groove(A) The surface of the MHC-binding groove in the ls6 complex is colored according to electrostatic potential (calculated in the absence of the peptide or bound water molecules); blue denotes positive potential and red indicates negative potential. Electrostatic analysis and surface display used program GRASP ([31]); the view of the peptide is similar to that of Figure 1.(B) The electrostatic potential surface of B53 in the HIV2 complex.

Figure 5.
Figure 5. The Peptide-Binding Surface of B53Peptide residues are colored red. The B53 main chain is represented schematically in blue and key side chains are shown in white; dashed lines indicate hydrogen bonds and, in (B) and (C), green spheres mark the positions of tightly bound water molecules.(A) Stereodiagram of the B pocket. The view is through the α1 helix.(B) The central region in the ls6 complex. The view for this and the following panels is through the α2 helix.(C) The central region in the HIV2 complex.(D) The F pocket, showing favorable ring stacking between the ls6 C-terminal (P9) peptide residue Phe and MHC residue Tyr123.

The above figures are reprinted by permission from Cell Press: Immunity (1996, 4, 215-228) copyright 1996.

Figures were selected by the author.