PDBsum entry 2bvq

Glycoprotein/peptide

PDB id

2bvq

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Contents

			Protein chains

					275 a.a. *


					99 a.a. *

			Ligands

					LYS-ALA-PHE-SER- PRO-GLU-VAL-ILE- PRO

			Waters ×297

* Residue conservation analysis

PDB id:

2bvq

Links

Name:

Glycoprotein/peptide

Title:

Structures of three HIV-1 hla-b5703-peptide complexes and identification of related hlas potentially associated with long-term non-progression

Structure:

Hla class i histocompatibility antigen, b-57 alpha chain. Chain: a. Fragment: residues 25-300. Synonym: mhc class i antigen b 57, Bw-57, hla-b5703. Engineered: yes. Beta-2-microglobulin. Chain: b. Fragment: residues 21-119. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes. Human immunodeficiency virus. Organism_taxid: 12721

Biol. unit:

Trimer (from PDB file)

Resolution:

2.00Å

R-factor:

0.208

R-free:

0.267

Authors:

G.B.Stewart-Jones,G.Gillespie,I.M.Overton,R.Kaul,P.Roche, A.J.Mcmichael,S.Rowland-Jones,E.Y.Jones

Key ref:

G.B.Stewart-Jones et al. (2005). Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression. J Immunol, 175, 2459-2468. PubMed id: 16081817

Date:

01-Jul-05

Release date:

07-Sep-05

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:					362 a.a. 275 a.a.*

Protein chain

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

Seq: Struc:					119 a.a. 99 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 28 residue positions (black crosses)

	J Immunol 175:2459-2468 (2005)
PubMed id: 16081817

Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression.
G.B.Stewart-Jones, G.Gillespie, I.M.Overton, R.Kaul, P.Roche, A.J.McMichael, S.Rowland-Jones, E.Y.Jones.

ABSTRACT

Long-term nonprogression during acute HIV infection has been strongly associated with HLA-B*5701 or HLA-B*5703. In this study, we present the high resolution crystal structures of HLA-B*5703 complexes with three HIV-1 epitopes: ISPRTLNAW (ISP), KAFSPEVIPMF (KAF-11), and KAFSPEVI (KAF-8). These reveal peptide anchoring at position 2 and their C termini. The different peptide lengths and primary sequences are accommodated by variation in the specific contacts made to the HLA-B*5703, flexibility in water structure, and conformational adjustment of side chains within the peptide-binding groove. The peptides adopt markedly different conformations, and trap variable numbers of water molecules, near a cluster of tyrosine side chains located in the central region of the peptide-binding groove. The KAF-11 epitope completely encompasses the shorter KAF-8 epitope but the peptides are presented in different conformations; the KAF-11 peptide arches out of the peptide-binding groove, exposing a significant main chain surface area. Bioinformatic analysis of the MHC side chains observed to contribute to the peptide anchor specificity, and other specific peptide contacts, reveals HLA alleles associated with long-term nonprogression and a number of related HLA alleles that may share overlapping peptide repertoires with HLA-B*5703 and thus may display a similar capacity for efficient immune control of HIV-1 infection.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20727150

L.Zhang, W.Li, L.Song, and L.Chen (2010).
A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations.

BMC Med Genomics, 3, 38.

20089717

M.Lacerda, K.Scheffler, and C.Seoighe (2010).
Epitope discovery with phylogenetic hidden Markov models.

Mol Biol Evol, 27, 1212-1220.

19450129

C.Bowman, and O.Delrieu (2009).
Immunogenetics of drug-induced skin blistering disorders. Part II: synthesis.

Pharmacogenomics, 10, 779-816.

20008523

J.Huang, J.J.Goedert, E.J.Sundberg, T.D.Cung, P.S.Burke, M.P.Martin, L.Preiss, J.Lifson, M.Lichterfeld, M.Carrington, and X.G.Yu (2009).
HLA-B*35-Px-mediated acceleration of HIV-1 infection by increased inhibitory immunoregulatory impulses.

J Exp Med, 206, 2959-2966.

18549801

D.Chessman, L.Kostenko, T.Lethborg, A.W.Purcell, N.A.Williamson, Z.Chen, L.Kjer-Nielsen, N.A.Mifsud, B.D.Tait, R.Holdsworth, C.A.Almeida, D.Nolan, W.A.Macdonald, J.K.Archbold, A.D.Kellerher, D.Marriott, S.Mallal, M.Bharadwaj, J.Rossjohn, and J.McCluskey (2008).
Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity.

Immunity, 28, 822-832.

PDB code:

2rfx

18057233

H.O.Peters, M.G.Mendoza, R.E.Capina, M.Luo, X.Mao, M.Gubbins, N.J.Nagelkerke, I.Macarthur, B.B.Sheardown, J.Kimani, C.Wachihi, S.Thavaneswaran, and F.A.Plummer (2008).
An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort.

J Virol, 82, 1980-1992.

18684953

J.Tang, W.Shao, Y.J.Yoo, I.Brill, J.Mulenga, S.Allen, E.Hunter, and R.A.Kaslow (2008).
Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples.

J Immunol, 181, 2626-2635.

18207719

S.Gras, L.Kjer-Nielsen, S.R.Burrows, J.McCluskey, and J.Rossjohn (2008).
T-cell receptor bias and immunity.

Curr Opin Immunol, 20, 119-125.

17121793

X.G.Yu, M.Lichterfeld, S.Chetty, K.L.Williams, S.K.Mui, T.Miura, N.Frahm, M.E.Feeney, Y.Tang, F.Pereyra, M.X.Labute, K.Pfafferott, A.Leslie, H.Crawford, R.Allgaier, W.Hildebrand, R.Kaslow, C.Brander, T.M.Allen, E.S.Rosenberg, P.Kiepiela, M.Vajpayee, P.A.Goepfert, M.Altfeld, P.J.Goulder, and B.D.Walker (2007).
Mutually exclusive T-cell receptor induction and differential susceptibility to human immunodeficiency virus type 1 mutational escape associated with a two-amino-acid difference between HLA class I subtypes.

J Virol, 81, 1619-1631.

16731944

A.Lazaryan, E.Lobashevsky, J.Mulenga, E.Karita, S.Allen, J.Tang, and R.A.Kaslow (2006).
Human leukocyte antigen B58 supertype and human immunodeficiency virus type 1 infection in native Africans.

J Virol, 80, 6056-6060.

16522810

C.Pastori, B.Weiser, C.Barassi, C.Uberti-Foppa, S.Ghezzi, R.Longhi, G.Calori, H.Burger, K.Kemal, G.Poli, A.Lazzarin, and L.Lopalco (2006).
Long-lasting CCR5 internalization by antibodies in a subset of long-term nonprogressors: a possible protective effect against disease progression.

Blood, 107, 4825-4833.

17013988

E.J.Im, J.P.Nkolola, K.di Gleria, A.J.McMichael, and T.Hanke (2006).
Induction of long-lasting multi-specific CD8+ T cells by a four-component DNA-MVA/HIVA-RENTA candidate HIV-1 vaccine in rhesus macaques.

Eur J Immunol, 36, 2574-2584.

16297661

S.R.Burrows, J.Rossjohn, and J.McCluskey (2006).
Have we cut ourselves too short in mapping CTL epitopes?

Trends Immunol, 27, 11-16.

17142892

T.Blicher, J.S.Kastrup, L.�.�.Pedersen, S.Buus, and M.Gajhede (2006).
Structure of HLA-A*1101 in complex with a hepatitis B peptide homologue.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1179-1184.

PDB code:

2hn7

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.