PDBsum entry 3e6f

Immune system

PDB id

3e6f

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Contents

			Protein chains

					273 a.a. *


					99 a.a. *

			Ligands

					ILE-GLY-PRO-GLY- ARG-ALA-PHE-TYR- ALA

			Waters ×125

* Residue conservation analysis

PDB id:

3e6f

Links

Name:

Immune system

Title:

Mhc class i h-2dd heavy chain complexed with beta-2 microglobulin and a variant peptide, pa9, from the human immunodeficiency virus (bal) envelope glycoprotein 120

Structure:

H-2 class i histocompatibility antigen, d-d alpha chain. Chain: a. Fragment: unp residues 26 to 298. Synonym: h-2d(d). Engineered: yes. Beta-2 microglobulin. Chain: b. Fragment: unp residues 21 to 119. Engineered: yes.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: h2-d1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: b2m, rp23-34e24.5-001. Synthetic: yes. Human immunodeficiency virus 1.

Resolution:

2.41Å

R-factor:

0.223

R-free:

0.271

Authors:

R.Wang,K.Natarajan,H.Robinson,D.H.Margulies

Key ref:

M.Honda et al. (2009). Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity. J Immunol, 183, 2425-2434. PubMed id: 19620307

Date:

15-Aug-08

Release date:

18-Aug-09

PROCHECK

	Headers

	References

Protein chain

P01900 (HA12_MOUSE) - H-2 class I histocompatibility antigen, D-D alpha chain from Mus musculus

Seq: Struc:					365 a.a. 273 a.a.

Protein chain

P01887 (B2MG_MOUSE) - Beta-2-microglobulin from Mus musculus

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

Key:

PfamA domain

Secondary structure

CATH domain

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

	J Immunol 183:2425-2434 (2009)
PubMed id: 19620307

Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.
M.Honda, R.Wang, W.P.Kong, M.Kanekiyo, W.Akahata, L.Xu, K.Matsuo, K.Natarajan, H.Robinson, T.E.Asher, D.A.Price, D.C.Douek, D.H.Margulies, G.J.Nabel.

ABSTRACT

Prime-boost immunization with gene-based vectors has been developed to generate more effective vaccines for AIDS, malaria, and tuberculosis. Although these vectors elicit potent T cell responses, the mechanisms by which they stimulate immunity are not well understood. In this study, we show that immunization by a single gene product, HIV-1 envelope, with alternative vector combinations elicits CD8(+) cells with different fine specificities and kinetics of mobilization. Vaccine-induced CD8(+) T cells recognized overlapping third V region loop peptides. Unexpectedly, two anchor variants bound H-2D(d) better than the native sequences, and clones with distinct specificities were elicited by alternative vectors. X-ray crystallography revealed major differences in solvent exposure of MHC-bound peptide epitopes, suggesting that processed HIV-1 envelope gave rise to MHC-I/peptide conformations recognized by distinct CD8(+) T cell populations. These findings suggest that different gene-based vectors generate peptides with alternative conformations within MHC-I that elicit distinct T cell responses after vaccination.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21422297

L.Flatz, R.Roychoudhuri, M.Honda, A.Filali-Mouhim, J.P.Goulet, N.Kettaf, M.Lin, M.Roederer, E.K.Haddad, R.P.Sékaly, and G.J.Nabel (2011).
Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines.

Proc Natl Acad Sci U S A, 108, 5724-5729.

20331477

C.K.Baumgartner, and L.P.Malherbe (2010).
Regulation of CD4 T-cell receptor diversity by vaccine adjuvants.

Immunology, 130, 16-22.

19884330

M.A.Durward, J.Harms, D.M.Magnani, L.Eskra, and G.A.Splitter (2010).
Discordant Brucella melitensis antigens yield cognate CD8+ T cells in vivo.

Infect Immun, 78, 168-176.

20468055

M.Rosario, A.Bridgeman, E.D.Quakkelaar, M.F.Quigley, B.J.Hill, M.L.Knudsen, V.Ammendola, K.Ljungberg, N.Borthwick, E.J.Im, A.J.McMichael, J.W.Drijfhout, H.Y.Greenaway, V.Venturi, D.C.Douek, S.Colloca, P.Liljeström, A.Nicosia, D.A.Price, C.J.Melief, and T.Hanke (2010).
Long peptides induce polyfunctional T cells against conserved regions of HIV-1 with superior breadth to single-gene vaccines in macaques.

Eur J Immunol, 40, 1973-1984.

20822348

R.M.Paris, J.H.Kim, M.L.Robb, and N.L.Michael (2010).
Prime-boost immunization with poxvirus or adenovirus vectors as a strategy to develop a protective vaccine for HIV-1.

Expert Rev Vaccines, 9, 1055-1069.

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.