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Yorodumi- EMDB-10464: Structure of Drosophila melanogaster Dispatched bound to a modifi... -
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-Basic information
Entry | Database: EMDB / ID: EMD-10464 | |||||||||
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Title | Structure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II | |||||||||
Map data | Drosophila melanogaster Dispatched bound to modified Hedgehog ligand HhN-C85II | |||||||||
Sample |
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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 / self proteolysis / germ cell migration / embryonic pattern specification / intein-mediated protein splicing / positive regulation of protein localization to cell surface / cell fate specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / regulation of mitotic cell cycle / protein autoprocessing / transmembrane transporter activity / endocytic vesicle / epidermis development / negative regulation of proteolysis / transmembrane transport / regulation of gene expression / heart development / peptidase activity / cytoplasmic vesicle / endosome / Hydrolases; Acting on ester bonds / calcium ion binding / extracellular space / extracellular region / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.76 Å | |||||||||
Authors | Korkhov VM / Cannac F | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10464.map.gz | 99.3 MB | EMDB map data format | |
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Header (meta data) | emd-10464-v30.xml emd-10464.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10464_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_10464.png | 61.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10464 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10464 | HTTPS FTP |
-Validation report
Summary document | emd_10464_validation.pdf.gz | 322.1 KB | Display | EMDB validaton report |
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Full document | emd_10464_full_validation.pdf.gz | 321.3 KB | Display | |
Data in XML | emd_10464_validation.xml.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10464 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10464 | HTTPS FTP |
-Related structure data
Related structure data | 6td6MC 6tbuC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10464.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Drosophila melanogaster Dispatched bound to modified Hedgehog ligand HhN-C85II | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : A complex of Dispatched and HhN-C85II in digitonin micelle
Entire | Name: A complex of Dispatched and HhN-C85II in digitonin micelle |
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Components |
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-Supramolecule #1: A complex of Dispatched and HhN-C85II in digitonin micelle
Supramolecule | Name: 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
Supramolecule | Name: Drosophila melanogaster protein Dispatched / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Drosophila melanogaster Hedgehog, HhN-C85II
Supramolecule | Name: Drosophila melanogaster Hedgehog, HhN-C85II / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Protein dispatched
Macromolecule | Name: Protein dispatched / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 139.149875 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Protein hedgehog
Macromolecule | Name: 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 |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 52.217121 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 51.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |