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Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR

Source organism: Homo sapiens
Biochemical function: not assigned
Biological process: antigen processing and presentation
Cellular component: MHC class II protein complex

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EC 5.3.1.1: Triose-phosphate isomerase

Reaction catalysed:
D-glyceraldehyde 3-phosphate = glycerone phosphate
Systematic name:
D-glyceraldehyde-3-phosphate aldose-ketose-isomerase
Alternative Name(s):
  • D-glyceraldehyde-3-phosphate ketol-isomerase
  • Phosphotriose isomerase
  • Triose phosphate mutase
  • Triose phosphoisomerase
  • Triosephosphate isomerase
  • Triosephosphate mutase

EC 4.2.3.3: Methylglyoxal synthase

Reaction catalysed:
Glycerone phosphate = methylglyoxal + phosphate
Systematic name:
Glycerone-phosphate phosphate-lyase (methylglyoxal-forming)
Alternative Name(s):
  • Glycerone-phosphate phospho-lyase
  • Methylglyoxal synthetase

GO terms

Biochemical function:
  • not assigned
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF07654
Domain description: Immunoglobulin C1-set domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor beta constant 1
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF07654 (Immunoglobulin C1-set domain) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF07654 (Immunoglobulin C1-set domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF07654 (Immunoglobulin C1-set domain) in T cell receptor beta constant 1. Showing 1 copy in chain E [auth D].

PF09291
Domain description: Domain of unknown function (DUF1968)
Occurring in:
  1. T cell receptor alpha chain constant
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF09291 (Domain of unknown function (DUF1968)) in T cell receptor alpha chain constant. Showing 1 copy in chain D [auth C].

PF00969
Domain description: Class II histocompatibility antigen, beta domain
Occurring in:
  1. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF00969 (Class II histocompatibility antigen, beta domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.

PF00993
Domain description: Class II histocompatibility antigen, alpha domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
The deposited structure of PDB entry 2iam contains 1 copy of Pfam domain PF00993 (Class II histocompatibility antigen, alpha domain) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR003597
Domain description: Immunoglobulin C1-set
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor beta constant 1
IPR036179
Domain description: Immunoglobulin-like domain superfamily
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor alpha chain constant
  4. T cell receptor beta constant 1
IPR013783
Domain description: Immunoglobulin-like fold
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor alpha chain constant
  4. T cell receptor beta constant 1
IPR007110
Domain description: Immunoglobulin-like domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor alpha chain constant
  4. T cell receptor beta constant 1
IPR015370
Domain description: T-cell receptor alpha chain, constant domain
Occurring in:
  1. T cell receptor alpha chain constant
IPR013106
Domain description: Immunoglobulin V-set domain
Occurring in:
  1. T cell receptor alpha chain constant
  2. T cell receptor beta constant 1
IPR003599
Domain description: Immunoglobulin subtype
Occurring in:
  1. T cell receptor alpha chain constant
  2. T cell receptor beta constant 1
IPR000353
Domain description: MHC class II, beta chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DRB1 beta chain
IPR003006
Domain description: Immunoglobulin/major histocompatibility complex, conserved site
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR001003
Domain description: MHC class II, alpha chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
IPR011162
Domain description: MHC classes I/II-like antigen recognition protein
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
IPR014745
Domain description: MHC class II, alpha/beta chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain

Structure domains

CATH CATH domains
2.60.40.10
Class: Mainly Beta
Architecture: Sandwich
Topology: Immunoglobulin-like
Homology: Immunoglobulins
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
  3. T cell receptor alpha chain constant
  4. T cell receptor beta constant 1
The deposited structure of PDB entry 2iam contains 1 copy of CATH domain 2.60.40.10 (Immunoglobulin-like) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 2iam contains 1 copy of CATH domain 2.60.40.10 (Immunoglobulin-like) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.
The deposited structure of PDB entry 2iam contains 2 copies of CATH domain 2.60.40.10 (Immunoglobulin-like) in T cell receptor alpha chain constant. Showing 2 copies in chain D [auth C].
The deposited structure of PDB entry 2iam contains 2 copies of CATH domain 2.60.40.10 (Immunoglobulin-like) in T cell receptor beta constant 1. Showing 2 copies in chain E [auth D].
3.10.320.10
Class: Alpha Beta
Architecture: Roll
Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 2iam contains 1 copy of CATH domain 3.10.320.10 (Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 2iam contains 1 copy of CATH domain 3.10.320.10 (Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.
SCOP SCOP annotations
48942
Class: All beta proteins
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Immunoglobulin
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 2iam contains 1 copy of SCOP domain 48942 (C1 set domains (antibody constant domain-like)) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 2iam contains 1 copy of SCOP domain 48942 (C1 set domains (antibody constant domain-like)) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.
54453
Class: Alpha and beta proteins (a+b)
Fold: MHC antigen-recognition domain
Superfamily: MHC antigen-recognition domain
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha chain
  2. HLA class II histocompatibility antigen, DRB1 beta chain
The deposited structure of PDB entry 2iam contains 1 copy of SCOP domain 54453 (MHC antigen-recognition domain) in HLA class II histocompatibility antigen, DR alpha chain. Showing 1 copy in chain A.
The deposited structure of PDB entry 2iam contains 1 copy of SCOP domain 54453 (MHC antigen-recognition domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain B.

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