› 4p2r

X-ray diffraction
3.3Å resolution

Crystal structure of the 5cc7 TCR in complex with 5c1/I-Ek

Released:
DOI: 10.2210/pdb4p2r/pdb
PDB entry 4p2r coloured by chain, front view.
PDB entry 4p2r coloured by chain, side view.
PDB entry 4p2r coloured by chain, top view.
Source organisms:
Primary publication:
Deconstructing the peptide-MHC specificity of T cell recognition.
Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, Ozkan E, Davis MM, Wucherpfennig KW, Garcia KC
Cell 157 1073-87 (2014)
PMID: 24855945

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-208997 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
H-2 class II histocompatibility antigen, E-K alpha chain Chains: A, F, K, P
Molecule details ›
Chains: A, F, K, P
Length: 204 amino acids
Theoretical weight: 23.62 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P04224 (Residues: 26-216; Coverage: 83%)
Sequence domains:
Structure domains:
Ig-like domain-containing protein Chains: B, G, L, Q
Molecule details ›
Chains: B, G, L, Q
Length: 212 amino acids
Theoretical weight: 24.43 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q31163 (Residues: 29-224; Coverage: 82%)
Gene name: H2-Eb1
Sequence domains:
Structure domains:
5c1 peptide Chains: C, H, M, R
Molecule details ›
Chains: C, H, M, R
Length: 13 amino acids
Theoretical weight: 1.38 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21(DE3)
5cc7 T-cell receptor alpha chain Chains: D, I, N, S
Molecule details ›
Chains: D, I, N, S
Length: 205 amino acids
Theoretical weight: 22.77 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
Structure domains: Immunoglobulins
5cc7 T-cell receptor beta chain Chains: E, J, O, T
Molecule details ›
Chains: E, J, O, T
Length: 266 amino acids
Theoretical weight: 29.61 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2
Unit cell:
a: 261.601Å b: 101.867Å c: 214.642Å
α: 90° β: 94.89° γ: 90°
R-values:
R R work R free
0.213 0.212 0.243
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)
  • Escherichia coli BL21

Quick links

Citations

112 review citations

The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy.
Havel et al. (2019)
111 more

7 mentions without citation

The perception and response of T cells to a changing environment are based on the law of initial value.
Huseby et al. (2022)
6 more