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

X-ray diffraction
2.8Å resolution
PDB entry 2ian coloured by chain, front view.
PDB entry 2ian coloured by chain, side view.
PDB entry 2ian coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1
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Multimeric state: hetero pentamer
Accessible surface area: 35720.42 Å2
Buried surface area: 14000.34 Å2
Dissociation area: 1,265.45 Å2
Dissociation energy (ΔGdiss): -0.61 kcal/mol
Dissociation entropy (TΔSdiss): 13.88 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134726
Assembly 2
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Multimeric state: hetero pentamer
Accessible surface area: 36159.81 Å2
Buried surface area: 14019.84 Å2
Dissociation area: 1,254.35 Å2
Dissociation energy (ΔGdiss): -2.36 kcal/mol
Dissociation entropy (TΔSdiss): 13.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134726
Assembly 3 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 36386.5 Å2
Buried surface area: 14017.46 Å2
Dissociation area: 1,258.69 Å2
Dissociation energy (ΔGdiss): -1.5 kcal/mol
Dissociation entropy (TΔSdiss): 13.91 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134726
Assembly 4
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Multimeric state: hetero pentamer
Accessible surface area: 36354.92 Å2
Buried surface area: 14072.17 Å2
Dissociation area: 1,253.13 Å2
Dissociation energy (ΔGdiss): -2.22 kcal/mol
Dissociation entropy (TΔSdiss): 13.91 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134726

Macromolecules

HLA class II histocompatibility antigen, DR alpha chain
Chains: A, F, K, P
Length: 182 amino acids
Theoretical weight: 21.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
Gene names: HLA-DRA, HLA-DRA1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ian, assembly 3, front view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ian, assembly 3, side view.
HLA class II histocompatibility antigen, DR alpha chain in PDB entry 2ian, assembly 3, top view.
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HLA class II histocompatibility antigen, DRB1 beta chain
Chains: B, G, L, Q
Length: 190 amino acids
Theoretical weight: 22.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01911 (Residues: 30-219; Coverage: 80%)
Gene name: HLA-DRB1
Pfam:
InterPro:
CATH:
SCOP:
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ian, assembly 3, front view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ian, assembly 3, side view.
HLA class II histocompatibility antigen, DRB1 beta chain in PDB entry 2ian, assembly 3, top view.
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Triosephosphate isomerase
Chains: C, H, M, R
Length: 15 amino acids
Theoretical weight: 1.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P60174 (Residues: 23-37; Coverage: 6%)
Gene names: TPI, TPI1
Triosephosphate isomerase in PDB entry 2ian, assembly 3, front view.
Triosephosphate isomerase in PDB entry 2ian, assembly 3, side view.
Triosephosphate isomerase in PDB entry 2ian, assembly 3, top view.
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T cell receptor alpha chain constant
Chains: D, I, N, S
Length: 202 amino acids
Theoretical weight: 22.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Pfam: Domain of unknown function (DUF1968)
InterPro:
CATH: Immunoglobulins
T cell receptor alpha chain constant in PDB entry 2ian, assembly 3, front view.
T cell receptor alpha chain constant in PDB entry 2ian, assembly 3, side view.
T cell receptor alpha chain constant in PDB entry 2ian, assembly 3, top view.
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T cell receptor beta constant 1
Chains: E, J, O, T
Length: 240 amino acids
Theoretical weight: 27.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01850 (Residues: 1-129; Coverage: 73%)
Gene name: TRBC1
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
T cell receptor beta constant 1 in PDB entry 2ian, assembly 3, front view.
T cell receptor beta constant 1 in PDB entry 2ian, assembly 3, side view.
T cell receptor beta constant 1 in PDB entry 2ian, assembly 3, top view.
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