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- EMDB-10464: Structure of Drosophila melanogaster Dispatched bound to a modifi... -

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Basic information

Entry
Database: EMDB / ID: EMD-10464
TitleStructure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II
Map dataDrosophila melanogaster Dispatched bound to modified Hedgehog ligand HhN-C85II
Sample
  • Complex: A complex of Dispatched and HhN-C85II in digitonin micelle
    • Complex: Drosophila melanogaster protein Dispatched
      • Protein or peptide: Protein dispatched
    • Complex: Drosophila melanogaster Hedgehog, HhN-C85II
      • Protein or peptide: Protein hedgehog
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / cell-cell signaling involved in cell fate commitment / Assembly of the 'signalling complexes' / gonadal mesoderm development / compound eye photoreceptor cell differentiation / wing disc pattern formation / 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 / foregut morphogenesis / cholesterol-protein transferase activity / imaginal disc-derived wing morphogenesis / compartment pattern specification / glial cell migration / developmental pigmentation / patched binding / germ cell migration / self proteolysis / embryonic pattern specification / positive regulation of protein localization to cell surface / intein-mediated protein splicing / cell fate specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / protein autoprocessing / transmembrane transporter activity / endocytic vesicle / epidermis development / regulation of mitotic cell cycle / negative regulation of proteolysis / transmembrane transport / heart development / peptidase activity / cytoplasmic vesicle / regulation of gene expression / Hydrolases; Acting on ester bonds / endosome / calcium ion binding / extracellular space / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein dispatched / 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. ...Protein dispatched / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.76 Å
AuthorsKorkhov VM / Cannac F
Funding support Switzerland, 1 items
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, 2019-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6td6
  • Surface level: 2.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6td6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10464.png

Downloads & links

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Map

FileDownload / File: emd_10464.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila melanogaster Dispatched bound to modified Hedgehog ligand HhN-C85II
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.3
Minimum - Maximum-6.2886877 - 10.486273
Average (Standard dev.)-0.014106185 (±0.47297862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z267.520267.520267.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-6.28910.486-0.014

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Supplemental data

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Sample components

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Entire : A complex of Dispatched and HhN-C85II in digitonin micelle

EntireName: A complex of Dispatched and HhN-C85II in digitonin micelle
Components
  • Complex: A complex of Dispatched and HhN-C85II in digitonin micelle
    • Complex: Drosophila melanogaster protein Dispatched
      • Protein or peptide: Protein dispatched
    • Complex: Drosophila melanogaster Hedgehog, HhN-C85II
      • Protein or peptide: Protein hedgehog
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: A complex of Dispatched and HhN-C85II in digitonin micelle

SupramoleculeName: A complex of Dispatched and HhN-C85II in digitonin micelle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Drosophila melanogaster protein Dispatched

SupramoleculeName: Drosophila melanogaster protein Dispatched / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Drosophila melanogaster Hedgehog, HhN-C85II

SupramoleculeName: Drosophila melanogaster Hedgehog, HhN-C85II / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Protein dispatched

MacromoleculeName: Protein dispatched / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 139.149875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLCFDSERMN WYYHVLARRP YLVVVSIAVY CVACIIVALV LNKLPDFSDP TLGFETRGTK IGERLTAWYN LLQETDHHGA LFSNPSDLW ERRRVEQGYV ETKLHPNHRR RKNKHKNRNK NKRRKEQNQS SHEHHDVAQK MMQFKKRLKA TSSPSPNLGF D TWIGDSGV ...String:
MLCFDSERMN WYYHVLARRP YLVVVSIAVY CVACIIVALV LNKLPDFSDP TLGFETRGTK IGERLTAWYN LLQETDHHGA LFSNPSDLW ERRRVEQGYV ETKLHPNHRR RKNKHKNRNK NKRRKEQNQS SHEHHDVAQK MMQFKKRLKA TSSPSPNLGF D TWIGDSGV FRDYEITNDS ASSSLEPTRR TEQIEYGHNT TSVDEEEHQQ RVQTKKSTWR LLKQAATLPT DGWADMHRRQ PI EGFFCDS SPRKEYSHFV VQRIGPNATD SLFDLNGLLA MCQLQDQITE VPSYRAFCEP EMLTTECCRP WSLPNYAAML ANK SSCFDL TTEDVTSLHT LLLGCYEYFH DLKMDNHCNE IPHCRAPEEC KRLNIVFNVL NFLTDFSFIK SNDSNVYLKY AMIF IPVAQ SNRLLPLFHE WEDVELINEL VEVVAMDLGL ENELFNELLL TDVWLVSLGG TFVMASVWLY TGSAFITLMS CVAIC FSLG LAYFFYAIVL EFEFFPYMNL LAVVVIIGIG ADDVFLFLKI WHCVLTERFS NRCTLTTQSQ SALPTLENSD HTESLE NIM ALTMRHAAAS MFVTSLTTAG AFYASYSSSI TAIKCFGIFA GTVVVTNYLL MITWLPASVS IMERLFATRM SCHHPMS IK LIHACKKSIN RFCQMFEECI TKSIMNYAYL WLLIFGALGA SSAVIVFWYP GLQLPEKSHF QLFVSKHPFE VYSSLKQQ F WFEKPLQAYY NFKMHMHFVW GVQAVDDGDY TNPNSYGHLH YDNNFNVSSR PAQLWILDFC QSVRQQPFYK ETLGMLLPN CFIENLIDYM KRRCIDDMDS TRKDRSPCCD AQFPFEPHIF EYCLPQSISN MYDTTFFRPG VAGPKFAEAP RLETEDYLGM SGNESAEYS TNGSFTPLLV KALVIEFESN VAYSTIYANI RQFYESVEHW FQMQLKTAPP ELQGGWFTSD LKFYNVQDTL S HDTFVAIC LAMAASLAVL LCFTVNILIS IYAVLTVSLS IFNTVAVLIL LGWQLNILES IAVSTAIGLA VDFSLHYGIH YR MSPVKER LAATQFVLSR IIGPTVMAAT TTGLAGGIMM ASNILPYIQI GVFLVVVMIV SWFYATFFLM SLLRVAGPQH GFL ELKWPL WSKRSSGSSK FYERKPSQVI ASEQLLTPTS SAIVELANSE THELESLNSN SLIKTISGIE SAHALSSLPR DFEH SFQTM HECKYQTYPS TSN

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Macromolecule #2: Protein hedgehog

MacromoleculeName: Protein hedgehog / type: protein_or_peptide / ID: 2
Details: 6xHis-Sumo-tagged HhN-C85II, N terminal fragment of Hedgehog
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 52.217121 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDNHSSVPWA SAASVTCLSL DAKCHSSSSS SSSKSAASSI SAIPQEETQT MRHIAHTQRC LSRLTSLVAL LLIVLPMVFS PAHSCGPGR GLGRHRARNL YPLVLKQTIP NLSEYTNSAS GPLEGVIRRD SPKFKDLVPN YNRDILFRDE EGTGADRLMS K RCKEKLNV ...String:
MDNHSSVPWA SAASVTCLSL DAKCHSSSSS SSSKSAASSI SAIPQEETQT MRHIAHTQRC LSRLTSLVAL LLIVLPMVFS PAHSCGPGR GLGRHRARNL YPLVLKQTIP NLSEYTNSAS GPLEGVIRRD SPKFKDLVPN YNRDILFRDE EGTGADRLMS K RCKEKLNV LAYSVMNEWP GIRLLVTESW DEDYHHGQES LHYEGRAVTI ATSDRDQSKY GMLARLAVEA GFDWVSYVSR RH IYCSVKS DSSISSHVHG CFTPESTALL ESGVRKPLGE LSIGDRVLSM TANGQAVYSE VILFMDRNLE QMQNFVQLHT DGG AVLTVT PAHLVSVWQP ESQKLTFVFA DRIEEKNQVL VRDVETGELR PQRVVKVGSV RSKGVVAPLT REGTIVVNSV AASC YAVIN SQSLAHWGLA PMRLLSTLEA WLPAKEQLHS SPKVVSSAQQ QNGIHWYANA LYKVKDYVLP QSWRHD

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 51.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 98623
FSC plot (resolution estimation)

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