7RPK

Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog

• PDB DOI:  https://doi.org/10.2210/pdb7RPK/pdb
• EM Map EMD-24617: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2021-08-03 Released: 2021-10-27 
• Deposition Author(s): Asarnow, D., Wang, Q., Ding, K., Cheng, Y., Beachy, P.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dispatched uses Na + flux to power release of lipid-modified Hedgehog.

Wang, Q., Asarnow, D.E., Ding, K., Mann, R.K., Hatakeyama, J., Zhang, Y., Ma, Y., Cheng, Y., Beachy, P.A.

(2021) Nature 599: 320-324

• PubMed: 34707294 
• DOI: https://doi.org/10.1038/s41586-021-03996-0
• Primary Citation of Related Structures:  
  7RPH, 7RPI, 7RPJ, 7RPK


• PubMed Abstract: 
  

The Dispatched protein, which is related to the NPC1 and PTCH1 cholesterol transporters ^1,2 and to H ⁺ -driven transporters of the RND family ^3,4 , enables tissue-patterning activity of the lipid-modified Hedgehog protein by releasing it from tightly -localized sites of embryonic expression ^5-10 . Here we determine a cryo-electron microscopy structure of the mouse protein Dispatched homologue 1 (DISP1), revealing three Na ⁺ ions coordinated within a channel that traverses its transmembrane domain. We find that the rate of Hedgehog export is dependent on the Na ⁺ gradient across the plasma membrane. The transmembrane channel and Na ⁺ binding are disrupted in DISP1-NNN, a variant with asparagine substitutions for three intramembrane aspartate residues that each coordinate and neutralize the charge of one of the three Na ⁺ ions. DISP1-NNN and variants that disrupt single Na ⁺ sites retain binding to, but are impaired in export of the lipid-modified Hedgehog protein to the SCUBE2 acceptor. Interaction of the amino-terminal signalling domain of the Sonic hedgehog protein (ShhN) with DISP1 occurs via an extensive buried surface area and contacts with an extended furin-cleaved DISP1 arm. Variability analysis reveals that ShhN binding is restricted to one extreme of a continuous series of DISP1 conformations. The bound and unbound DISP1 conformations display distinct Na ⁺ -site occupancies, which suggests a mechanism by which transmembrane Na ⁺ flux may power extraction of the lipid-linked Hedgehog signal from the membrane. Na ⁺ -coordinating residues in DISP1 are conserved in PTCH1 and other metazoan RND family members, suggesting that Na ⁺ flux powers their conformationally driven activities.

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Organizational Affiliation: 

Departments of Urology, and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, immunoprecipitation

Macromolecule Content

• Total Structure Weight: 187.27 kDa 
• Atom Count: 10,018 
• Modelled Residue Count: 1,104 
• Deposited Residue Count: 1,516 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dispatched homolog 1	A	1,352	Mus musculus	Mutation(s): 0  Gene Names: Disp1, Disp, Dispa, Icb, Icbins Membrane Entity: Yes
UniProt
Find proteins for Q3TDN0 (Mus musculus) Explore Q3TDN0  Go to UniProtKB:  Q3TDN0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sonic hedgehog protein	B [auth H]	164	Mus musculus	Mutation(s): 0  Gene Names: Shh, Hhg1 EC: 3.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q62226 (Mus musculus) Explore Q62226  Go to UniProtKB:  Q62226
IMPC:  MGI:98297

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AV0 (Subject of Investigation/LOI)	CA [auth A], DA [auth A]	2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside C47 H88 O22 MADJBYLAYPCCOO-VWHTXWAPSA-N
Y01 (Subject of Investigation/LOI)	AA [auth A], BA [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
6OE	GA [auth A]	(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate C17 H34 N O8 P PELYUHWUVHDSSU-HNNXBMFYSA-N
NAG	HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	PA [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	OA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	MA [auth H], NA [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	EA [auth A], FA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-27 
Deposition Author(s): Asarnow, D., Wang, Q., Ding, K., Cheng, Y., Beachy, P.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM102498
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM140847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	S10OD021741
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2021-10-27
  Type: Initial release
  
• Version 1.1: 2021-11-10
  Changes: Database references
• Version 1.2: 2021-11-24
  Changes: Database references