7RHR | pdb_00007rhr

Cryo-EM structure of Xenopus Patched-1 in nanodisc

• PDB DOI: https://doi.org/10.2210/pdb7RHR/pdb
• EM Map EMD-24467: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Xenopus calcaratus
• Expression System: Insecta environmental sample
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2021-07-18 Released: 2022-03-02 
• Deposition Author(s): Huang, P., Lian, T., Jiang, J., Salic, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for catalyzed assembly of the Sonic hedgehog-Patched1 signaling complex.

Huang, P., Wierbowski, B.M., Lian, T., Chan, C., Garcia-Linares, S., Jiang, J., Salic, A.

(2022) Dev Cell 57: 670-685.e8

• PubMed: 35231446 
• DOI: https://doi.org/10.1016/j.devcel.2022.02.008
• Primary Citation Related Structures: 
  7RHQ, 7RHR


• PubMed Abstract: 
  

  The dually lipidated Sonic hedgehog (SHH) morphogen signals through the tumor suppressor membrane protein Patched1 (PTCH1) to activate the Hedgehog pathway, which is fundamental in development and cancer. SHH engagement with PTCH1 requires the GAS1 coreceptor, but the mechanism is unknown. We demonstrate a unique role for GAS1, catalyzing SHH-PTCH1 complex assembly in vertebrate cells by direct SHH transfer from the extracellular SCUBE2 carrier to PTCH1. Structure of the GAS1-SHH-PTCH1 transition state identifies how GAS1 recognizes the SHH palmitate and cholesterol modifications in modular fashion and how it facilitates lipid-dependent SHH handoff to PTCH1. Structure-guided experiments elucidate SHH movement from SCUBE2 to PTCH1, explain disease mutations, and demonstrate that SHH-induced PTCH1 dimerization causes its internalization from the cell surface. These results define how the signaling-competent SHH-PTCH1 complex assembles, the key step triggering the Hedgehog pathway, and provide a paradigm for understanding morphogen reception and its regulation.

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Organizational Affiliation: 
• Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Laboratory of Membrane Proteins and Structural Biology, Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: [e-mail].
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 136.65 kDa 
• Atom Count: 7,820 
• Modeled Residue Count: 974 
• Deposited Residue Count: 1,205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Patched-1	A	1,205	Xenopus calcaratus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q98SW6 (Xenopus laevis) Explore Q98SW6  Go to UniProtKB:  Q98SW6
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	C [auth A], D [auth A], G [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Huang, P., Lian, T., Jiang, J., Salic, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM122920

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-03-09
  Changes: Database references
• Version 1.2: 2022-03-23
  Changes: Database references
• Version 1.3: 2024-10-09
  Changes: Data collection, Structure summary