› 4p4k

X-ray diffraction
2.8Å resolution

Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic hypersensitivity and auto immunity

Released:
DOI: 10.2210/pdb4p4k/pdb
PDB entry 4p4k coloured by chain, front view.
PDB entry 4p4k coloured by chain, side view.
PDB entry 4p4k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity.
Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW
Cell 158 132-42 (2014)
PMID: 24995984

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-105339 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class II histocompatibility antigen, DP alpha 1 chain Chains: A, E
Molecule details ›
Chains: A, E
Length: 183 amino acids
Theoretical weight: 21.17 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P20036 (Residues: 32-214; Coverage: 79%)
Gene names: HLA-DP1A, HLA-DPA1, HLASB
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DP beta 1 chain Chains: B, F
Molecule details ›
Chains: B, F
Length: 212 amino acids
Theoretical weight: 24.39 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: P04440 (Residues: 16-17, 32-218; Coverage: 76%)
Gene names: HLA-DP1B, HLA-DPB1
Sequence domains:
Structure domains:
T cell receptor alpha chain constant Chains: C, G
Molecule details ›
Chains: C, G
Length: 209 amino acids
Theoretical weight: 23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01848 (Residues: 1-93; Coverage: 66%)
Gene names: TCRA, TRAC
Sequence domains: Domain of unknown function (DUF1968)
Structure domains: Immunoglobulins
T cell receptor beta constant 2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 242 amino acids
Theoretical weight: 27.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A5B9 (Residues: 1-129; Coverage: 73%)
Gene names: TCRBC2, TRBC2
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NAG 5 x NAG
Ligand NA 2 x NA
Ligand 0BE 2 x 0BE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P212121
Unit cell:
a: 79.4Å b: 137.24Å c: 213.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.252
Expression systems:
  • unidentified baculovirus
  • Escherichia coli

Quick links

Citations

23 review citations

T cell antigen receptor recognition of antigen-presenting molecules.
Rossjohn et al. (2015)
22 more

10 mentions without citation

The Many Faces of CD4+ T Cells: Immunological and Structural Characteristics.
Chatzileontiadou et al. (2020)
9 more