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- PDB-6td6: Structure of Drosophila melanogaster Dispatched bound to a modifi... -

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Basic information

Entry
Database: PDB / ID: 6td6
TitleStructure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II
Components
  • Protein dispatched
  • Protein hedgehog
KeywordsMEMBRANE PROTEIN / RND transporter / Dispatched / Hedgehog / transmembrane domain / ectodomain / cholesteryl hemisuccinate / detergent micelle / digitonin / monomer
Function / homology
Function and homology information


progression of morphogenetic furrow involved in compound eye morphogenesis / negative regulation of homotypic cell-cell adhesion / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell ...progression of morphogenetic furrow involved in compound eye morphogenesis / negative regulation of homotypic cell-cell adhesion / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell / Ligand-receptor interactions / leg disc morphogenesis / Formation and transport of the N-HH ligand / cytoneme / regulation of epithelial cell migration, open tracheal system / morphogenesis of larval imaginal disc epithelium / Assembly of the 'signalling complexes' / gonadal mesoderm development / cell-cell signaling involved in cell fate commitment / wing disc pattern formation / compound eye photoreceptor cell differentiation / Hedgehog ligand biogenesis / analia development / anterior head segmentation / patched ligand maturation / posterior head segmentation / imaginal disc growth / anterior/posterior lineage restriction, imaginal disc / epithelial cell migration, open tracheal system / trunk segmentation / heart formation / genital disc development / genital disc anterior/posterior pattern formation / compound eye morphogenesis / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / morphogen activity / mucosal immune response / hindgut morphogenesis / segment polarity determination / ventral midline development / cholesterol-protein transferase activity / foregut morphogenesis / imaginal disc-derived wing morphogenesis / compartment pattern specification / developmental pigmentation / glial cell migration / patched binding / embryonic pattern specification / germ cell migration / self proteolysis / intein-mediated protein splicing / positive regulation of protein localization to cell surface / cell fate specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / transmembrane transporter activity / protein autoprocessing / endocytic vesicle / epidermis development / regulation of mitotic cell cycle / negative regulation of proteolysis / heart development / peptidase activity / regulation of gene expression / cytoplasmic vesicle / Hydrolases; Acting on ester bonds / endosome / calcium ion binding / extracellular space / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Protein patched/dispatched / Patched family ...: / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily
Similarity search - Domain/homology
Protein hedgehog / Protein dispatched
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.76 Å
AuthorsKorkhov, V.M. / Cannac, F.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation150665 & 176992 Switzerland
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structure of the Hedgehog release protein Dispatched.
Authors: Fabien Cannac / Chao Qi / Julia Falschlunger / George Hausmann / Konrad Basler / Volodymyr M Korkhov /
Abstract: The Hedgehog (Hh) signaling pathway controls embryonic development and adult tissue homeostasis in multicellular organisms. In , the pathway is primed by secretion of a dually lipid-modified ...The Hedgehog (Hh) signaling pathway controls embryonic development and adult tissue homeostasis in multicellular organisms. In , the pathway is primed by secretion of a dually lipid-modified morphogen, Hh, a process dependent on a membrane-integral protein Dispatched. Although Dispatched is a critical component of the pathway, the structural basis of its activity has, so far, not been described. Here, we describe a cryo-electron microscopy structure of the Dispatched at 3.2-Å resolution. The ectodomains of Dispatched adopt an open conformation suggestive of a receptor-chaperone role. A three-dimensional reconstruction of Dispatched bound to Hh confirms the ability of Dispatched to bind Hh but using a unique mode distinct from those previously observed in structures of Hh complexes. The structure may represent the state of the complex that precedes shedding of Hh from the surface of the morphogen-releasing cell.
History
DepositionNov 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Protein dispatched
B: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,0134
Polymers191,3672
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2030 Å2
ΔGint10 kcal/mol
Surface area50870 Å2
MethodPISA

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Components

#1: Protein Protein dispatched


Mass: 139149.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Homo sapiens (human) / References: UniProt: Q9VNJ5
#2: Protein Protein hedgehog


Mass: 52217.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6xHis-Sumo-tagged HhN-C85II, N terminal fragment of Hedgehog
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: hh, CG4637 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: Q02936
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1A complex of Dispatched and HhN-C85II in digitonin micelleCOMPLEX#1-#20MULTIPLE SOURCES
2Drosophila melanogaster protein DispatchedCOMPLEX#11RECOMBINANT
3Drosophila melanogaster Hedgehog, HhN-C85IICOMPLEX#21RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Drosophila melanogaster (fruit fly)7227
23Drosophila melanogaster (fruit fly)7227
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELION3initial Euler assignment
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98623 / Symmetry type: POINT

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