6TD6

Structure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II

• PDB DOI: https://doi.org/10.2210/pdb6TD6/pdb
• EM Map EMD-10464: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2019-11-07 Released: 2020-06-03 
• Deposition Author(s): Korkhov, V.M., Cannac, F.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 192.01 kDa 
• Atom Count: 7,914 
• Modelled Residue Count: 982 
• Deposited Residue Count: 1,689 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dispatched	A	1,218	Drosophila melanogaster	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q9VNJ5 (Drosophila melanogaster) Explore Q9VNJ5  Go to UniProtKB:  Q9VNJ5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein hedgehog	B	471	Drosophila melanogaster	Mutation(s): 0  Gene Names: hh, CG4637 Membrane Entity: Yes
UniProt
Find proteins for Q02936 (Drosophila melanogaster) Explore Q02936  Go to UniProtKB:  Q02936

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 4.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Korkhov, V.M., Cannac, F.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	150665 & 176992

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-06-17
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary