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- EMDB-10452: Structure of Drosophila melanogaster Dispatched -

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Basic information

Entry
Database: EMDB / ID: EMD-10452
TitleStructure of Drosophila melanogaster Dispatched
Map dataDrosophila melanogaster Dispatched
Sample
  • Complex: Drosophila melanogaster protein Dispatched (disp)
    • Protein or peptide: Protein dispatched
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Formation and transport of the N-HH ligand / cytoneme / wing disc pattern formation / : / patched ligand maturation / segment polarity determination / smoothened signaling pathway / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
Protein dispatched / Protein patched/dispatched / Patched family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 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 4, 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: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tbu
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10452.png

Downloads & links

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Map

FileDownload / File: emd_10452.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila melanogaster Dispatched
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.04071731 - 0.07844124
Average (Standard dev.)0.0000850566 (±0.001553409)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 246.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z304304304
origin x/y/z0.0000.0000.000
length x/y/z246.240246.240246.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS304304304
D min/max/mean-0.0410.0780.000

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Supplemental data

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Sample components

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Entire : Drosophila melanogaster protein Dispatched (disp)

EntireName: Drosophila melanogaster protein Dispatched (disp)
Components
  • Complex: Drosophila melanogaster protein Dispatched (disp)
    • Protein or peptide: Protein dispatched
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Drosophila melanogaster protein Dispatched (disp)

SupramoleculeName: Drosophila melanogaster protein Dispatched (disp) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 139 KDa

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Macromolecule #1: Protein dispatched

MacromoleculeName: Protein dispatched / type: protein_or_peptide / ID: 1
Details: Drosophila melanogaster Dispatched, tagged with a C-terminal 3C-protease cleavage site, YFP and twin-strep tag.
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 #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 9 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

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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
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 9216 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: The initial model was generated using preliminary data collected with Jeol JEM2200 microscope.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 286136
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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