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Crystal structure of the B1 TCR in complex with HLA-DP4-Ply

X-ray diffraction
3.4Å resolution
PDB entry 7t2d coloured by chain, front view.
PDB entry 7t2d coloured by chain, side view.
PDB entry 7t2d coloured by chain, top view.
Source organisms:
Assembly composition:
hetero pentamer (preferred)
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero pentamer
Accessible surface area: 37871.58 Å2
Buried surface area: 15223.3 Å2
Dissociation area: 1,014.6 Å2
Dissociation energy (ΔGdiss): -4.19 kcal/mol
Dissociation entropy (TΔSdiss): 13.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134735
Assembly 2
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Multimeric state: hetero pentamer
Accessible surface area: 37800.54 Å2
Buried surface area: 15344.9 Å2
Dissociation area: 992.79 Å2
Dissociation energy (ΔGdiss): -3.48 kcal/mol
Dissociation entropy (TΔSdiss): 13.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134735
Assembly 3
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Multimeric state: hetero pentamer
Accessible surface area: 38042.1 Å2
Buried surface area: 14851.48 Å2
Dissociation area: 1,004.57 Å2
Dissociation energy (ΔGdiss): -1.39 kcal/mol
Dissociation entropy (TΔSdiss): 13.87 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134735
Assembly 4
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Multimeric state: hetero pentamer
Accessible surface area: 38098.7 Å2
Buried surface area: 14940.06 Å2
Dissociation area: 989.54 Å2
Dissociation energy (ΔGdiss): -1.42 kcal/mol
Dissociation entropy (TΔSdiss): 13.87 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134735

Macromolecules

HLA class II histocompatibility antigen, DP alpha 1 chain
Chains: A, F, K, P
Length: 181 amino acids
Theoretical weight: 20.94 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P20036 (Residues: 32-212; Coverage: 78%)
Gene names: HLA-DP1A, HLA-DPA1, HLASB
Pfam:
InterPro:
HLA class II histocompatibility antigen, DP alpha 1 chain in PDB entry 7t2d, assembly 1, front view.
HLA class II histocompatibility antigen, DP alpha 1 chain in PDB entry 7t2d, assembly 1, side view.
HLA class II histocompatibility antigen, DP alpha 1 chain in PDB entry 7t2d, assembly 1, top view.
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HLA class II histocompatibility antigen, DP beta 1 chain
Chains: B, G, L, Q
Length: 188 amino acids
Theoretical weight: 21.92 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P04440 (Residues: 30-217; Coverage: 82%)
Gene names: HLA-DP1B, HLA-DPB1
Pfam:
InterPro:
HLA class II histocompatibility antigen, DP beta 1 chain in PDB entry 7t2d, assembly 1, front view.
HLA class II histocompatibility antigen, DP beta 1 chain in PDB entry 7t2d, assembly 1, side view.
HLA class II histocompatibility antigen, DP beta 1 chain in PDB entry 7t2d, assembly 1, top view.
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Pneumolysin
Chains: C, H, M, R
Length: 15 amino acids
Theoretical weight: 1.83 KDa
Source organism: Streptococcus pneumoniae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q04IN8 (Residues: 429-441; Coverage: 3%)
Gene names: SPD_1726, ply
Pneumolysin in PDB entry 7t2d, assembly 1, front view.
Pneumolysin in PDB entry 7t2d, assembly 1, side view.
Pneumolysin in PDB entry 7t2d, assembly 1, top view.
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T cell receptor alpha chain constant
Chains: D, I, N, S
Length: 207 amino acids
Theoretical weight: 23.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Pfam: Domain of unknown function (DUF1968)
InterPro:
T cell receptor alpha chain constant in PDB entry 7t2d, assembly 1, front view.
T cell receptor alpha chain constant in PDB entry 7t2d, assembly 1, side view.
T cell receptor alpha chain constant in PDB entry 7t2d, assembly 1, top view.
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T cell receptor beta constant 1
Chains: E, J, O, T
Length: 243 amino acids
Theoretical weight: 27.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01850 (Residues: 1-129; Coverage: 73%)
Gene name: TRBC1
Pfam: Immunoglobulin C1-set domain
InterPro:
T cell receptor beta constant 1 in PDB entry 7t2d, assembly 1, front view.
T cell receptor beta constant 1 in PDB entry 7t2d, assembly 1, side view.
T cell receptor beta constant 1 in PDB entry 7t2d, assembly 1, top view.
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