PDBsum entry 1tmc

Histocompatibility antigen

PDB id

1tmc

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Contents

			Protein chains

					175 a.a. *


					99 a.a. *

			Ligands

					GLU-VAL-ALA-PRO- PRO-GLU-TYR-HIS- ARG-LYS

			Waters ×98

* Residue conservation analysis

PDB id:

1tmc

Links

Name:

Histocompatibility antigen

Title:

The three-dimensional structure of a class i major histocompatibility complex molecule missing the alpha3 domain of the heavy chain

Structure:

Class i histocompatibility antigen (hla-aw68). Chain: a. Engineered: yes. Beta 2-microglobulin. Chain: b. Engineered: yes. Decameric peptide (evappeyhrk). Chain: c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: beta-2-microglobulin. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å

R-factor:

0.207

Authors:

E.J.Collins,D.N.Garboczi,M.N.Karpusas,D.C.Wiley

Key ref:

E.J.Collins et al. (1995). The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain. Proc Natl Acad Sci U S A, 92, 1218-1221. PubMed id: 7862664 DOI: 10.1073/pnas.92.4.1218

Date:

19-Dec-94

Release date:

31-Mar-95

PROCHECK

	Headers

	References

Protein chain

P04439 (1A03_HUMAN) - HLA class I histocompatibility antigen, A alpha chain from Homo sapiens

Seq: Struc:					365 a.a. 175 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 10 residue positions (black crosses)

DOI no: 10.1073/pnas.92.4.1218	Proc Natl Acad Sci U S A 92:1218-1221 (1995)
PubMed id: 7862664

The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain.
E.J.Collins, D.N.Garboczi, M.N.Karpusas, D.C.Wiley.

ABSTRACT

Class I major histocompatibility complex (MHC) molecules are ternary complexes of the soluble serum protein beta 2-microglobulin, MHC heavy chain, and bound peptide. The first two domains (alpha 1, alpha 2) of the heavy chain create the peptide binding cleft and the surface that contacts the T-cell receptor. The third domain (alpha 3) associates with the T-cell co-receptor, CD8, during T-cell recognition. Here we describe the x-ray crystal structure of a human class I MHC molecule, HLA-Aw68, from which the alpha 3 domain has been proteolytically removed. The resulting molecule shows no gross morphological changes compared to the intact protein. A decameric peptide complexed with the intact HLA-Aw68 is seen to bind to the proteolized molecule in the conventional manner, demonstrating that the alpha 3 domain is not required for the structural integrity of the molecule or for peptide binding.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18451549

H.Nojima, M.Takeda-Shitaka, K.Kanou, K.Kamiya, and H.Umeyama (2008).
Dynamic interaction among the platform domain and two membrane-proximal immunoglobulin-like domains of class I major histocompatibility complex: normal mode analysis.

Chem Pharm Bull (Tokyo), 56, 635-641.

16352655

E.Duprat, M.P.Lefranc, and O.Gascuel (2006).
A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin.

Bioinformatics, 22, 453-459.

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

16186824

F.E.Tynan, S.R.Burrows, A.M.Buckle, C.S.Clements, N.A.Borg, J.J.Miles, T.Beddoe, J.C.Whisstock, M.C.Wilce, S.L.Silins, J.M.Burrows, L.Kjer-Nielsen, L.Kostenko, A.W.Purcell, J.McCluskey, and J.Rossjohn (2005).
T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide.

Nat Immunol, 6, 1114-1122.

PDB code:

2ak4

16041067

T.Blicher, J.S.Kastrup, S.Buus, and M.Gajhede (2005).
High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide.

Acta Crystallogr D Biol Crystallogr, 61, 1031-1040.

PDB code:

1x7q

12913229

H.Nojima, M.Takeda-Shitaka, Y.Kurihara, K.Kamiya, and H.Umeyama (2003).
Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex.

Chem Pharm Bull (Tokyo), 51, 923-928.

12010576

P.E.Adrian, G.Rajaseger, V.S.Mathura, M.K.Sakharkar, and P.Kangueane (2002).
Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data.

BMC Struct Biol, 2, 2.

10852379

M.García-Peydró, D.Rognan, and J.A.López de Castro (2000).
Limited plasticity in the recognition of peptide epitope variants by an alloreactive CTL clone correlates directly with conservation of critical residues and inversely with peptide length.

Tissue Antigens, 55, 289-295.

11045629

O.Schueler-Furman, Y.Altuvia, A.Sette, and H.Margalit (2000).
Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles.

Protein Sci, 9, 1838-1846.

10607669

K.Maenaka, and E.Y.Jones (1999).
MHC superfamily structure and the immune system.

Curr Opin Struct Biol, 9, 745-753.

9700508

E.J.Collins, and J.A.Frelinger (1998).
Altered peptide ligand design: altering immune responses to class I MHC/peptide complexes.

Immunol Rev, 163, 151-160.

9039778

E.Y.Jones (1997).
MHC class I and class II structures.

Curr Opin Immunol, 9, 75-79.

9316393

M.A.Batalia, and E.J.Collins (1997).
Peptide binding by class I and class II MHC molecules.

Biopolymers, 43, 281-302.

8729452

D.H.Fremont, W.A.Rees, and H.Kozono (1996).
Biophysical studies of T-cell receptors and their ligands.

Curr Opin Immunol, 8, 93.

8624811

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

PDB code:

1a1n

8778210

J.C.Solheim, J.R.Cook, and T.H.Hansen (1995).
Conformational changes induced in the MHC class I molecule by peptide and beta 2-microglobulin.

Immunol Res, 14, 200-217.

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.