PDBsum entry 3dx7

Immune system

PDB id

3dx7

Loading ...

Contents

			Protein chains

					276 a.a. *


					99 a.a. *

			Ligands

					GLU-GLU-ASN-LEU- LEU-ASP-PHE-VAL- ARG-PHE


					ACT ×4


					GOL ×2

			Waters ×401

* Residue conservation analysis

PDB id:

3dx7

Links

Name:

Immune system

Title:

Crystal structure of hla-b 4403 Presenting 10mer ebv antigen

Structure:

Hla class i histocompatibility complex hla-b 4403. Chain: a. Synonym: hla class i histocompatibility antigen, b-44 alpha chain . Mhc class i antigen b 44. Bw-44. Engineered: yes. Beta-2-microglobulin. Chain: b. Synonym: beta-2-microglobulin form pi 5.3. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-b, hlab. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: b2m, cdabp0092, hdcma22p. Synthetic: yes. Other_details: sequence occurs in human herpesvirus 4, gene ebna6,

Resolution:

1.60Å

R-factor:

0.184

R-free:

0.210

Authors:

J.K.Archbold,L.K.Ely,J.Rossjohn

Key ref:

J.K.Archbold et al. (2009). Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition. J Exp Med, 206, 209-219. PubMed id: 19139173

Date:

23-Jul-08

Release date:

27-Jan-09

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:					362 a.a. 276 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 31 residue positions (black crosses)

	J Exp Med 206:209-219 (2009)
PubMed id: 19139173

Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.
J.K.Archbold, W.A.Macdonald, S.Gras, L.K.Ely, J.J.Miles, M.J.Bell, R.M.Brennan, T.Beddoe, M.C.Wilce, C.S.Clements, A.W.Purcell, J.McCluskey, S.R.Burrows, J.Rossjohn.

ABSTRACT

Human leukocyte antigen (HLA) gene polymorphism plays a critical role in protective immunity, disease susceptibility, autoimmunity, and drug hypersensitivity, yet the basis of how HLA polymorphism influences T cell receptor (TCR) recognition is unclear. We examined how a natural micropolymorphism in HLA-B44, an important and large HLA allelic family, affected antigen recognition. T cell-mediated immunity to an Epstein-Barr virus determinant (EENLLDFVRF) is enhanced when HLA-B*4405 was the presenting allotype compared with HLA-B*4402 or HLA-B*4403, each of which differ by just one amino acid. The micropolymorphism in these HLA-B44 allotypes altered the mode of binding and dynamics of the bound viral epitope. The structure of the TCR-HLA-B*4405(EENLLDFVRF) complex revealed that peptide flexibility was a critical parameter in enabling preferential engagement with HLA-B*4405 in comparison to HLA-B*4402/03. Accordingly, major histocompatibility complex (MHC) polymorphism can alter the dynamics of the peptide-MHC landscape, resulting in fine-tuning of T cell responses between closely related allotypes.

Literature references that cite this PDB file's key reference

PubMed id

Reference

23154222

J.Rossjohn, D.G.Pellicci, O.Patel, L.Gapin, and D.I.Godfrey (2012).
Recognition of CD1d-restricted antigens by natural killer T cells.

Nat Rev Immunol, 12, 845-857.

21321209

G.P.Morris, P.P.Ni, and P.M.Allen (2011).
Alloreactivity is limited by the endogenous peptide repertoire.

Proc Natl Acad Sci U S A, 108, 3695-3700.

21439439

I.A.van der Mei, S.Simpson, J.Stankovich, and B.V.Taylor (2011).
Individual and joint action of environmental factors and risk of MS.

Neurol Clin, 29, 233-255.

21364947

J.M.Khan, and S.Ranganathan (2011).
Understanding TR Binding to pMHC Complexes: How Does a TR Scan Many pMHC Complexes yet Preferentially Bind to One.

PLoS One, 6, e17194.

21376639

K.S.Wun, G.Cameron, O.Patel, S.S.Pang, D.G.Pellicci, L.C.Sullivan, S.Keshipeddy, M.H.Young, A.P.Uldrich, M.S.Thakur, S.K.Richardson, A.R.Howell, P.A.Illarionov, A.G.Brooks, G.S.Besra, J.McCluskey, L.Gapin, S.A.Porcelli, D.I.Godfrey, and J.Rossjohn (2011).
A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells.

Immunity, 34, 327-339.

PDB codes:

3arb 3ard 3are 3arf 3arg

21301478

S.Gras, L.Kjer-Nielsen, Z.Chen, J.Rossjohn, and J.McCluskey (2011).
The structural bases of direct T-cell allorecognition: implications for T-cell-mediated transplant rejection.

Immunol Cell Biol, 89, 388-395.

21301481

S.R.Burrows, D.J.Moss, and R.Khanna (2011).
Understanding human T-cell-mediated immunoregulation through herpesviruses.

Immunol Cell Biol, 89, 352-358.

21297580

Y.Yin, Y.Li, M.C.Kerzic, R.Martin, and R.A.Mariuzza (2011).
Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection.

EMBO J, 30, 1137-1148.

PDB code:

3o6f

21124993

J.J.Miles, A.M.Bulek, D.K.Cole, E.Gostick, A.J.Schauenburg, G.Dolton, V.Venturi, M.P.Davenport, M.P.Tan, S.R.Burrows, L.Wooldridge, D.A.Price, P.J.Rizkallah, and A.K.Sewell (2010).
Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection.

PLoS Pathog, 6, e1001198.

PDB code:

3o4l

20139278

L.Dong, P.Li, T.Oenema, C.L.McClurkan, and D.M.Koelle (2010).
Public TCR use by herpes simplex virus-2-specific human CD8 CTLs.

J Immunol, 184, 3063-3071.

20122941

N.G.Walpole, L.Kjer-Nielsen, L.Kostenko, J.McCluskey, A.G.Brooks, J.Rossjohn, and C.S.Clements (2010).
The structure and stability of the monomorphic HLA-G are influenced by the nature of the bound peptide.

J Mol Biol, 397, 467-480.

PDB codes:

3kyn 3kyo

20566715

S.Gras, Z.Chen, J.J.Miles, Y.C.Liu, M.J.Bell, L.C.Sullivan, L.Kjer-Nielsen, R.M.Brennan, J.M.Burrows, M.A.Neller, R.Khanna, A.W.Purcell, A.G.Brooks, J.McCluskey, J.Rossjohn, and S.R.Burrows (2010).
Allelic polymorphism in the T cell receptor and its impact on immune responses.

J Exp Med, 207, 1555-1567.

PDB codes:

3mv7 3mv8 3mv9

19624567

C.Macedo, E.A.Orkis, I.Popescu, B.D.Elinoff, A.Zeevi, R.Shapiro, F.G.Lakkis, and D.Metes (2009).
Contribution of naïve and memory T-cell populations to the human alloimmune response.

Am J Transplant, 9, 2057-2066.

19366919

J.M.Blackwell, S.E.Jamieson, and D.Burgner (2009).
HLA and infectious diseases.

Clin Microbiol Rev, 22, 370.

19617574

M.Rist, C.Smith, M.J.Bell, S.R.Burrows, and R.Khanna (2009).
Cross-recognition of HLA DR4 alloantigen by virus-specific CD8+ T cells: a new paradigm for self-/nonself-recognition.

Blood, 114, 2244-2253.

20064447

O.Y.Borbulevych, K.H.Piepenbrink, B.E.Gloor, D.R.Scott, R.F.Sommese, D.K.Cole, A.K.Sewell, and B.M.Baker (2009).
T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.

Immunity, 31, 885-896.

PDB codes:

3h7b 3h9h 3h9s 3ixa

20064448

W.A.Macdonald, Z.Chen, S.Gras, J.K.Archbold, F.E.Tynan, C.S.Clements, M.Bharadwaj, L.Kjer-Nielsen, P.M.Saunders, M.C.Wilce, F.Crawford, B.Stadinsky, D.Jackson, A.G.Brooks, A.W.Purcell, J.W.Kappler, S.R.Burrows, J.Rossjohn, and J.McCluskey (2009).
T cell allorecognition via molecular mimicry.

Immunity, 31, 897-908.

PDB codes:

3kpl 3kpm 3kpn 3kpo 3kpp 3kpq 3kpr 3kps

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 codes are shown on the right.