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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3TDN0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q62226 (Mus musculus) Explore Q62226 Go to UniProtKB: Q62226
IMPC: MGI:98297
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q62226
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV0 (Subject of Investigation/LOI) Query on AV0 Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A]	CA [auth A], DA [auth A]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-VWHTXWAPSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A]
Y01 (Subject of Investigation/LOI) Query on Y01 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain W [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain W [auth A]	AA [auth A] BA [auth A] C [auth A] D [auth A] E [auth A] 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		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
6OE Query on 6OE Download Ideal Coordinates CCD File SDF format, chain GA [auth A] MOL2 format, chain GA [auth A]	GA [auth A]	(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate C₁₇ H₃₄ N O₈ P PELYUHWUVHDSSU-HNNXBMFYSA-N		Interactions Focus chain GA [auth A] Interactions & Density Focus chain GA [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A]	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		Interactions Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Interactions & Density Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain PA [auth H] MOL2 format, chain PA [auth H]	PA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain PA [auth H] Interactions & Density Focus chain PA [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain OA [auth H] MOL2 format, chain OA [auth H]	OA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain OA [auth H] Interactions & Density Focus chain OA [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain MA [auth H] SDF format, chain NA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H]	MA [auth H], NA [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain MA [auth H] Focus chain NA [auth H] Interactions & Density Focus chain MA [auth H] Focus chain NA [auth H]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A]	EA [auth A], FA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-27

Deposition Author(s):

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 (Full details and data files)

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
Version 1.3: 2023-12-13
Changes: Data collection, Derived calculations, Structure summary