6RMG

Structure of PTCH1 bound to a modified Hedgehog ligand ShhN-C24II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of sterol recognition by human hedgehog receptor PTCH1.

Qi, C.Di Minin, G.Vercellino, I.Wutz, A.Korkhov, V.M.

(2019) Sci Adv 5: eaaw6490-eaaw6490

  • DOI: 10.1126/sciadv.aaw6490

  • PubMed Abstract: 
  • Hedgehog signaling is central in embryonic development and tissue regeneration. Disruption of the pathway is linked to genetic diseases and cancer. Binding of the secreted ligand, Sonic hedgehog (ShhN) to its receptor Patched (PTCH1) activates the si ...

    Hedgehog signaling is central in embryonic development and tissue regeneration. Disruption of the pathway is linked to genetic diseases and cancer. Binding of the secreted ligand, Sonic hedgehog (ShhN) to its receptor Patched (PTCH1) activates the signaling pathway. Here, we describe a 3.4-Å cryo-EM structure of the human PTCH1 bound to ShhN C24II , a modified hedgehog ligand mimicking its palmitoylated form. The membrane-embedded part of PTCH1 is surrounded by 10 sterol molecules at the inner and outer lipid bilayer portion of the protein. The annular sterols interact at multiple sites with both the sterol-sensing domain (SSD) and the SSD-like domain (SSDL), which are located on opposite sides of PTCH1. The structure reveals a possible route for sterol translocation across the lipid bilayer by PTCH1 and homologous transporters.


    Organizational Affiliation

    Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein patched homolog 1,GFP-like fluorescent chromoprotein FP506, related
A
1471Eimeria acervulinaHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: PTCH1 (PTCH)
Find proteins for U6GSR1 (Eimeria acervulina)
Go to UniProtKB:  U6GSR1
Find proteins for Q13635 (Homo sapiens)
Go to Gene View: PTCH1
Go to UniProtKB:  Q13635
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sonic hedgehog protein
B
285Homo sapiensMutation(s): 0 
Gene Names: SHH
Find proteins for Q15465 (Homo sapiens)
Go to Gene View: SHH
Go to UniProtKB:  Q15465
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y01
Query on Y01

Download SDF File 
Download CCD File 
A
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-05-06 
  • Released Date: 2019-10-09 
  • Deposition Author(s): Korkhov, V.M., Qi, C.

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland150665

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release