› 4bkf

X-ray diffraction
4.65Å resolution

crystal structure of the human EphA4 ectodomain in complex with human ephrinB3

Released:
DOI: 10.2210/pdb4bkf/pdb
PDB entry 4bkf coloured by chain, front view.
PDB entry 4bkf coloured by chain, side view.
PDB entry 4bkf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structurally encoded intraclass differences in EphA clusters drive distinct cell responses.
Seiradake E, Schaupp A, del Toro Ruiz D, Kaufmann R, Mitakidis N, Harlos K, Aricescu AR, Klein R, Jones EY
Nat Struct Mol Biol 20 958-64 (2013)
PMID: 23812375

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157100 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ephrin type-A receptor 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 568 amino acids
Theoretical weight: 62.68 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P54764 (Residues: 20-547; Coverage: 55%)
Gene names: EPHA4, HEK8, SEK, TYRO1
Sequence domains:
Ephrin-B3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 183 amino acids
Theoretical weight: 20.4 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q15768 (Residues: 27-169; Coverage: 45%)
Gene names: EFNB3, EPLG8, LERK8
Sequence domains: Ephrin

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24, DIAMOND BEAMLINE I04
Spacegroup: P4332
Unit cell:
a: 300.53Å b: 300.53Å c: 300.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.329 0.327 0.351
Expression system: Homo sapiens

Quick links

Citations

13 review citations

Mechanisms of ephrin-Eph signalling in development, physiology and disease.
Kania et al. (2016)
12 more

5 mentions without citation

Oligomerization and nanocluster organization render specificity.
Nussinov et al. (2015)
4 more