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Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd)

X-ray diffraction
2.69Å resolution
PDB entry 8tq8 coloured by chain, front view.
PDB entry 8tq8 coloured by chain, side view.
PDB entry 8tq8 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: 37434.72 Å2
Buried surface area: 10571.9 Å2
Dissociation area: 927.32 Å2
Dissociation energy (ΔGdiss): -7.81 kcal/mol
Dissociation entropy (TΔSdiss): 13.78 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279440
Assembly 2
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Multimeric state: hetero pentamer
Accessible surface area: 36469.95 Å2
Buried surface area: 10411.95 Å2
Dissociation area: 872.01 Å2
Dissociation energy (ΔGdiss): -7.93 kcal/mol
Dissociation entropy (TΔSdiss): 13.74 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-279440

Macromolecules

H-2 class I histocompatibility antigen, D-D alpha chain
Chains: A, C
Length: 273 amino acids
Theoretical weight: 31.82 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01900 (Residues: 26-298; Coverage: 80%)
Gene name: H2-D1
Pfam:
H-2 class I histocompatibility antigen, D-D alpha chain in PDB entry 8tq8, assembly 1, front view.
H-2 class I histocompatibility antigen, D-D alpha chain in PDB entry 8tq8, assembly 1, side view.
H-2 class I histocompatibility antigen, D-D alpha chain in PDB entry 8tq8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P01900  
127320406080100120140160180200220240260
 
100200
UniProt
P01900
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
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Beta-2-microglobulin
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Pfam: Immunoglobulin C1-set domain
Beta-2-microglobulin in PDB entry 8tq8, assembly 1, front view.
Beta-2-microglobulin in PDB entry 8tq8, assembly 1, side view.
Beta-2-microglobulin in PDB entry 8tq8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P01887  
199102030405060708090
 
50100IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
UniProt
P01887
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
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Surface protein gp120
Chains: E, P
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P04578 (Residues: 311-320; Coverage: 1%)
Gene name: env
Transmembrane protein gp41 in PDB entry 8tq8, assembly 1, front view.
Transmembrane protein gp41 in PDB entry 8tq8, assembly 1, side view.
Transmembrane protein gp41 in PDB entry 8tq8, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P04578  
11012345678910
 
510RGPGRAFVTI
UniProt
P04578
Chains
Interaction interfaces
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Fab.34.5.8 Heavy chain
Chains: F, H
Length: 219 amino acids
Theoretical weight: 23.33 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Fab.34.5.8 Heavy chain in PDB entry 8tq8, assembly 1, front view.
Fab.34.5.8 Heavy chain in PDB entry 8tq8, assembly 1, side view.
Fab.34.5.8 Heavy chain in PDB entry 8tq8, assembly 1, top view.
121920406080100120140160180200
 
100200
Chains
RSRZ Outlier Chain D (auth H)
Chain D (auth H)
RSRZ Outlier Chain I (auth F)
Chain I (auth F)
Secondary structure
Ligand binding sites
Interaction interfaces
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Fab.34.5.8 Light chain
Chains: G, L
Length: 219 amino acids
Theoretical weight: 24.21 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Fab.34.5.8 Light chain in PDB entry 8tq8, assembly 1, front view.
Fab.34.5.8 Light chain in PDB entry 8tq8, assembly 1, side view.
Fab.34.5.8 Light chain in PDB entry 8tq8, assembly 1, top view.
121920406080100120140160180200
 
100200
Chains
RSRZ Outlier Chain E (auth L)
Chain E (auth L)
RSRZ Outlier Chain J (auth G)
Chain J (auth G)
Secondary structure
Interaction interfaces
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