› 6rtw

X-ray diffraction
1.9Å resolution

Crystal structure of the Patched-1 (PTCH1) ectodomain in complex with nanobody NB64 and cholesterol-hemisuccinate

Released:
DOI: 10.2210/pdb6rtw/pdb
PDB entry 6rtw coloured by chain, front view.
PDB entry 6rtw coloured by chain, side view.
PDB entry 6rtw coloured by chain, top view.
Source organisms:
Primary publication:
The morphogen Sonic hedgehog inhibits its receptor Patched by a pincer grasp mechanism.
Rudolf AF, Kinnebrew M, Kowatsch C, Ansell TB, El Omari K, Bishop B, Pardon E, Schwab RA, Malinauskas T, Qian M, Duman R, Covey DF, Steyaert J, Wagner A, Sansom MSP, Rohatgi R, Siebold C
Nat Chem Biol 15 975-982 (2019)
PMID: 31548691

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212010 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein patched homolog 1 Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 34.14 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q13635 (Residues: 136-423; Coverage: 20%)
Gene names: PTCH, PTCH1
Llama-derived nanobody NB64 Chain: B
Molecule details ›
Chain: B
Length: 130 amino acids
Theoretical weight: 14.04 KDa
Source organism: Lama glama
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand NAG 3 x NAG
Ligand Y01 1 x Y01
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 47.26Å b: 65.72Å c: 151.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.23
Expression systems:
  • Homo sapiens
  • Escherichia coli

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Citations

14 review citations

Cholesterol access in cellular membranes controls Hedgehog signaling.
Radhakrishnan et al. (2020)
13 more