› 4kng

X-ray diffraction
2.5Å resolution

Crystal structure of human LGR5-RSPO1-RNF43

Released:
DOI: 10.2210/pdb4kng/pdb
PDB entry 4kng coloured by chain, front view.
PDB entry 4kng coloured by chain, side view.
PDB entry 4kng coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structural basis of R-spondin recognition by LGR5 and RNF43.
Chen PH, Chen X, Lin Z, Fang D, He X
Genes Dev 27 1345-50 (2013)
PMID: 23756651

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-130979 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Leucine-rich repeat-containing G-protein coupled receptor 5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 531 amino acids
Theoretical weight: 59.28 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O75473 (Residues: 32-557; Coverage: 59%)
Gene names: GPR49, GPR67, LGR5
Sequence domains:
Structure domains: Ribonuclease Inhibitor
R-spondin-1 Chains: M, P
Molecule details ›
Chains: M, P
Length: 115 amino acids
Theoretical weight: 12.36 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2MKA7 (Residues: 35-144; Coverage: 45%)
Gene name: RSPO1
Sequence domains: Furin-like repeat, cysteine-rich
Structure domains: Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
E3 ubiquitin-protein ligase RNF43 Chains: E, F
Molecule details ›
Chains: E, F
Length: 160 amino acids
Theoretical weight: 17.55 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q68DV7 (Residues: 44-198; Coverage: 20%)
Gene name: RNF43
Sequence domains: ZNRF-3 Ectodomain
Structure domains: Glucose Oxidase; domain 1

Ligands and Environments

2 bound ligands:
Ligand NAG 2 x NAG
Ligand NI 1 x NI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 104.575Å b: 120.971Å c: 181.009Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.232 0.276
Expression system: Homo sapiens

Quick links

Citations

25 review citations

Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration.
Barker N. (2014)
24 more

13 mentions without citation

The R-spondin/Lgr5/Rnf43 module: regulator of Wnt signal strength.
de Lau et al. (2014)
12 more