› 7rdv

X-ray diffraction
2.9Å resolution

TFH TCR bound to MHC Class II IAd presenting aggrecan epitope

Released:
DOI: 10.2210/pdb7rdv/pdb
PDB entry 7rdv coloured by chain, front view.
PDB entry 7rdv coloured by chain, side view.
PDB entry 7rdv coloured by chain, top view.
Source organisms:
Entry authors: Lim JJ, Rossjohn J, Reid H

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-224998 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
H-2 class II histocompatibility antigen, A-D alpha chain Chain: A
Molecule details ›
Chain: A
Length: 181 amino acids
Theoretical weight: 20.57 KDa
Source organism: Mus musculus
Expression system: Baculovirus expression vector pFastBac1-HM
UniProt:
  • Canonical: P04228 (Residues: 28-205; Coverage: 76%)
Gene name: H2-Aa
Sequence domains:
H-2 class II histocompatibility antigen, A-D beta chain Chain: B
Molecule details ›
Chain: B
Length: 186 amino acids
Theoretical weight: 21.85 KDa
Source organism: Mus musculus
Expression system: Baculovirus expression vector pFastBac1-HM
UniProt:
  • Canonical: P01921 (Residues: 31-216; Coverage: 78%)
Gene name: H2-Ab1
Sequence domains:
TFH TCR alpha chain Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 23.02 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
TFH TCR beta chain Chain: D
Molecule details ›
Chain: D
Length: 240 amino acids
Theoretical weight: 26.83 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
Aggrecan core protein Chain: H
Molecule details ›
Chain: H
Length: 12 amino acids
Theoretical weight: 1.37 KDa
Source organism: Homo sapiens
Expression system: Baculovirus expression vector pFastBac1-HM
UniProt:
  • Canonical: P16112 (Residues: 91-101; Coverage: 0%)
Gene names: ACAN, AGC1, CSPG1, MSK16

Ligands and Environments

1 bound ligand:
Ligand NAG 2 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P3121
Unit cell:
a: 102.562Å b: 102.562Å c: 195.695Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.239 0.237 0.265
Expression systems:
  • Baculovirus expression vector pFastBac1-HM
  • Escherichia coli BL21(DE3)

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