7E2G

Cryo-EM structure of hDisp1NNN-3C

PDB DOI: https://doi.org/10.2210/pdb7E2G/pdb
EM Map EMD-30956: EMDB EMDataResource

Classification: LIPID TRANSPORT
Organism(s): Homo sapiens
Expression System: Mammalian expression vector Flag-EGFP-MCS-pcDNA3.1
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2021-02-05 Released: 2021-12-08
Deposition Author(s): Li, W., Wang, L., Gong, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.61 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 insights into proteolytic activation of the human Dispatched1 transporter for Hedgehog morphogen release.

Li, W., Wang, L., Wierbowski, B.M., Lu, M., Dong, F., Liu, W., Li, S., Wang, P., Salic, A., Gong, X.

(2021) Nat Commun 12: 6966-6966

PubMed: 34845226 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-27257-w
Primary Citation of Related Structures:
7E2G, 7E2H, 7E2I

PubMed Abstract:
The membrane protein Dispatched (Disp), which belongs to the RND family of small molecule transporters, is essential for Hedgehog (Hh) signaling, by catalyzing the extracellular release of palmitate- and cholesterol-modified Hh ligands from producing cells. Disp function requires Furin-mediated proteolytic cleavage of its extracellular domain, but how this activates Disp remains obscure. Here, we employ cryo-electron microscopy to determine atomic structures of human Disp1 (hDisp1), before and after cleavage, and in complex with lipid-modified Sonic hedgehog (Shh) ligand. These structures, together with biochemical data, reveal that proteolytic cleavage opens the extracellular domain of hDisp1, removing steric hindrance to Shh binding. Structure-guided functional experiments demonstrate the role of hDisp1-Shh interactions in ligand release. Our results clarify the mechanisms of hDisp1 activation and Shh morphogen release, and highlight how a unique proteolytic cleavage event enabled acquisition of a protein substrate by a member of a family of small molecule transporters.

Organizational Affiliation

Department of Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.

Macromolecule Content

Total Structure Weight: 176.15 kDa
Atom Count: 7,376
Modelled Residue Count: 901
Deposited Residue Count: 1,518
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dispatched homolog 1,Protein dispatched homolog 1	A [auth D]	1,518	Homo sapiens	Mutation(s): 3 Gene Names: DISP1, DISPA Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F81 (Homo sapiens) Explore Q96F81 Go to UniProtKB: Q96F81
PHAROS: Q96F81 GTEx: ENSG00000154309
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96F81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 (Subject of Investigation/LOI) Query on Y01 Download Ideal Coordinates CCD File SDF format, chain B [auth D] SDF format, chain C [auth D] SDF format, chain D SDF format, chain E [auth D] SDF format, chain F [auth D] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain B [auth D] MOL2 format, chain C [auth D] MOL2 format, chain D MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D]	B [auth D] C [auth D] D E [auth D] F [auth D] B [auth D], C [auth D], D, E [auth D], F [auth D], G [auth D], H [auth D], I [auth D], J [auth D], K [auth D], L [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain B [auth D] Focus chain C [auth D] Focus chain D Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain B [auth D] Focus chain C [auth D] Focus chain D Focus chain E [auth D] Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	M [auth D], N [auth D], O [auth D], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]