PDBsum entry: 1b3j

Immune system

PDB-id: 1b3j

Biological unit = asymmetric unit, as shown
(as defined in PDB file)

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PROCHECK

Protein chain

264 a.a. *

Ligands

NAG-NAG

Waters ×52

* Residue conservation analysis

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PDB id:

1b3j

Name:

Immune system

Title:

Structure of the mhc class i homolog mic-a, a gammadelta t cell ligand

Structure:

Mhc class i homolog mic-a. Chain: a. Fragment: extracellular domain, residues 1 - 274. Synonym: mica, mic, perb11. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: extracellular. Gene: mica-001. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: hi5.

Biological unit:

Monomer (from PDB file)

UniProt:

Q29983 (MICA_HUMAN)

Seq:

Struc:

Seq:

383 a.a.

Struc:

264 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

3.00Å

R-factor:

0.246

R-free:

0.288

Authors:

P.Li,S.Willie,S.Bauer,D.Morris,T.Spies,R.Strong

Key ref:

P.Li et al. (1999). Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand.. Immunity, 10, 577-584. [PubMed id: 10367903] [DOI: 10.1016/S1074-7613(00)80057-6]

Date:

11-Dec-98

Release date:

09-Jul-99

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Clefts

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Key reference

DOI no: 10.1016/S1074-7613(00)80057-6

Immunity 10:577-584 (1999)

PubMed id: 10367903

Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand.

P.Li, S.T.Willie, S.Bauer, D.L.Morris, T.Spies, R.K.Strong.

ABSTRACT

The major histocompatibility complex (MHC) class I homolog MIC-A functions as a stress-inducible antigen that is recognized by a subset of gammadelta T cells independent of beta2-microglobulin and bound peptides. Its crystal structure reveals a dramatically altered MHC class I fold, both in detail and overall domain organization. The only remnant of a peptide-binding groove is a small cavity formed as the result of disordering a large section of one of the groove-defining helices. Loss of beta2-microglobulin binding is due to a restructuring of the interaction interfaces. Structural mapping of sequence variation suggests potential receptor binding sites on the underside of the platform on the side opposite of the surface recognized by alphabeta T cell receptors on MHC class I-peptide complexes.

Selected figure(s)

Figure 4.
Figure 4. Detailed Views of the “Latch” and the Crystallographic Dimer(A) Stereoview of a ribbon representation of the folds of MIC-A (blue) and HLA-B27 (green) in the region of helix 2b in the α2 domain highlighting the “latch.” The side chains of the latch residue (Val-95 in MIC-A and Gly-100 in HLA-B27) and the conserved disulfide bond (Cys-96/Cys-164) are shown in ball-and-stick representation.(B and C) A view from the side (B) and from the top (C) of the crystallographic dimer. The two MIC-A monomers, one in red and the other in blue, are shown as backbone ribbons. The ordered N-linked carbohydrate is shown in ball-and-stick representation, and the crystallographic dyad axis is indicated by the black oval. The C-termini of the two monomers are colored yellow.

Figure 5.
Figure 5. Space-Filling Representations of the Surface Character of MIC-A(A and B) A view of the back (A) and the side (B) of MIC-A highlighting the potential N-linked oligosaccharide sites present in all primate MIC alleles (orange) and those conserved in all primate MIC-A alleles (red). Residues shown in purple correspond to residues buried in a hypothetical complex with β[2]-m (see Figure 3).(C and D) Views of the equivalent of the peptide/TCR-binding surface of the platform domain (the “top,” [C]) and the β[2]-m binding surface of the platform domain (the “underside,” [D]; same orientation as in [A]) of MIC-A. Residues conserved across all primate MIC sequences are colored blue; residues where conservative substitutions have occurred (L/V/I, E/D, D/N, E/Q, E/N, or R/K) are colored green; nonconserved residues are colored yellow; residues in the α3 domain are colored gray. Two patches of conserved residues straddle the N-linked oligosaccharide at Asn-8: patch 1 (below Asn-8 in [D]): Ser-4, Arg-6, Glu-25, His-27, Gly-30, Gln-31, Pro-45, Trp-49, Glu-97, and Arg-180; patch 2 (above and to the left of Asn-8 in [D]); Leu-12, Lys-84, Leu-87, His-109, Tyr-111, Asp-113, Gly-114, Glu-115, Gln-131, and Ser-132. Residues at potential N-linked glycosylation sites are colored as in (A) and (B).

The above figures are reprinted by permission from Cell Press: Immunity (1999, 10, 577-584) copyright 1999.

Figures were selected by an automated process.