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Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule

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

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GO terms

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

Sequence families

Pfam Protein families (Pfam)
PF07686
Domain description: Immunoglobulin V-set domain
Occurring in:
  1. T-cell receptor alpha chain V region PHDS58
  2. Ig-like domain-containing protein
The deposited structure of PDB entry 2icw contains 2 copies of Pfam domain PF07686 (Immunoglobulin V-set domain) in T-cell receptor alpha chain V region PHDS58. Showing 1 copy in chain I.
The deposited structure of PDB entry 2icw contains 2 copies of Pfam domain PF07686 (Immunoglobulin V-set domain) in Ig-like domain-containing protein. Showing 1 copy in chain J.

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
The deposited structure of PDB entry 2icw contains 2 copies 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 2icw contains 2 copies of Pfam domain PF07654 (Immunoglobulin C1-set domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain E.

PF09245
Domain description: Mycoplasma arthritidis-derived mitogen
Occurring in:
  1. Superantigen
The deposited structure of PDB entry 2icw contains 2 copies of Pfam domain PF09245 (Mycoplasma arthritidis-derived mitogen) in Superantigen. Showing 1 copy in chain G.

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 2icw contains 2 copies of Pfam domain PF00969 (Class II histocompatibility antigen, beta domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain E.

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 2icw contains 2 copies 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
IPR013106
Domain description: Immunoglobulin V-set domain
Occurring in:
  1. T-cell receptor alpha chain V region PHDS58
  2. Ig-like domain-containing protein
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
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 V region PHDS58
  4. Ig-like domain-containing protein
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 V region PHDS58
  4. Ig-like domain-containing protein
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 V region PHDS58
  4. Ig-like domain-containing protein
IPR003599
Domain description: Immunoglobulin subtype
Occurring in:
  1. T-cell receptor alpha chain V region PHDS58
  2. Ig-like domain-containing protein
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
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
IPR001003
Domain description: MHC class II, alpha chain, N-terminal
Occurring in:
  1. HLA class II histocompatibility antigen, DR alpha 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
IPR042074
Domain description: Mycoplasma arthritidis-derived mitogen, C-terminal
Occurring in:
  1. Superantigen
IPR036342
Domain description: Superantigen MAM
Occurring in:
  1. Superantigen
IPR015326
Domain description: Mycoplasma arthritidis-derived mitogen
Occurring in:
  1. Superantigen

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 V region PHDS58
  4. Ig-like domain-containing protein
The deposited structure of PDB entry 2icw contains 2 copies 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 2icw contains 2 copies of CATH domain 2.60.40.10 (Immunoglobulin-like) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain E.
The deposited structure of PDB entry 2icw contains 2 copies of CATH domain 2.60.40.10 (Immunoglobulin-like) in T-cell receptor alpha chain V region PHDS58. Showing 1 copy in chain I.
The deposited structure of PDB entry 2icw contains 2 copies of CATH domain 2.60.40.10 (Immunoglobulin-like) in Ig-like domain-containing protein. Showing 1 copy in chain J.
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 2icw contains 2 copies 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 2icw contains 2 copies 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 E.
1.10.10.530
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: mam-mhc complex, Chain D, Domain 2
Occurring in:
  1. Superantigen
The deposited structure of PDB entry 2icw contains 2 copies of CATH domain 1.10.10.530 (Arc Repressor Mutant, subunit A) in Superantigen. Showing 1 copy in chain G.
1.20.120.390
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Four Helix Bundle (Hemerythrin (Met), subunit A)
Homology: Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1
Occurring in:
  1. Superantigen
The deposited structure of PDB entry 2icw contains 2 copies of CATH domain 1.20.120.390 (Four Helix Bundle (Hemerythrin (Met), subunit A)) in Superantigen. Showing 1 copy in chain G.
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 2icw contains 2 copies 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 2icw contains 2 copies 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 E.
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 2icw contains 2 copies 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 2icw contains 2 copies of SCOP domain 54453 (MHC antigen-recognition domain) in HLA class II histocompatibility antigen, DRB1 beta chain. Showing 1 copy in chain E.
48727
Class: All beta proteins
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Immunoglobulin
Occurring in:
  1. Ig-like domain-containing protein
The deposited structure of PDB entry 2icw contains 2 copies of SCOP domain 48727 (V set domains (antibody variable domain-like)) in Ig-like domain-containing protein. Showing 1 copy in chain J.
101345
Class: All alpha proteins
Fold: Superantigen MAM
Superfamily: Superantigen MAM
Occurring in:
  1. Superantigen
The deposited structure of PDB entry 2icw contains 2 copies of SCOP domain 101345 (Superantigen MAM) in Superantigen. Showing 1 copy in chain G.

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