› 6bga

X-ray diffraction
2.31Å resolution

2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide

Released:
DOI: 10.2210/pdb6bga/pdb
PDB entry 6bga coloured by chain, front view.
PDB entry 6bga coloured by chain, side view.
PDB entry 6bga coloured by chain, top view.
Source organisms:
Primary publication:
Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro.
Gee MH, Sibener LV, Birnbaum ME, Jude KM, Yang X, Fernandes RA, Mendoza JL, Glassman CR, Garcia KC
Proc Natl Acad Sci U S A 115 E7369-E7378 (2018)
PMID: 30021852

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-528189 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (6 distinct):
H-2 class II histocompatibility antigen, E-K alpha chain Chain: A
Molecule details ›
Chain: A
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 Chain: B
Molecule details ›
Chain: B
Length: 233 amino acids
Theoretical weight: 26.59 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:
T cell receptor 2B4 alpha chain Chain: C
Molecule details ›
Chain: C
Length: 220 amino acids
Theoretical weight: 24.1 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
Structure domains: Immunoglobulins
T cell receptor 2B4 beta chain Chain: D
Molecule details ›
Chain: D
Length: 255 amino acids
Theoretical weight: 29.01 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
Structure domains: Immunoglobulins
Velcro peptide Chain: E
Molecule details ›
Chain: E
Length: 15 amino acids
Theoretical weight: 1.31 KDa
Source organism: synthetic construct
Expression system: Trichoplusia ni

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand NAG 2 x NAG
Ligand EDO 3 x EDO
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Unit cell:
a: 79.107Å b: 58.851Å c: 224.619Å
α: 90° β: 91.71° γ: 90°
R-values:
R R work R free
0.195 0.192 0.237
Expression system: Trichoplusia ni

Quick links

Citations

7 review citations

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.
Lee et al. (2020)
6 more

2 mentions without citation

Molecular evolution of peptides by yeast surface display technology.
Linciano et al. (2019)
1 more