+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30956 | |||||||||
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Title | Cryo-EM structure of hDisp1NNN-3C | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information patched ligand maturation / diaphragm development / embryonic pattern specification / peptide transport / dorsal/ventral pattern formation / peptide transmembrane transporter activity / determination of left/right symmetry / smoothened signaling pathway / regulation of protein secretion / protein homotrimerization ...patched ligand maturation / diaphragm development / embryonic pattern specification / peptide transport / dorsal/ventral pattern formation / peptide transmembrane transporter activity / determination of left/right symmetry / smoothened signaling pathway / regulation of protein secretion / protein homotrimerization / basolateral plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Li W / Wang L / Gong X | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural insights into proteolytic activation of the human Dispatched1 transporter for Hedgehog morphogen release. Authors: Wanqiu Li / Linlin Wang / Bradley M Wierbowski / Mo Lu / Feitong Dong / Wenchen Liu / Sisi Li / Peiyi Wang / Adrian Salic / Xin Gong / Abstract: The membrane protein Dispatched (Disp), which belongs to the RND family of small molecule transporters, is essential for Hedgehog (Hh) signaling, by catalyzing the extracellular release of palmitate- ...The membrane protein Dispatched (Disp), which belongs to the RND family of small molecule transporters, is essential for Hedgehog (Hh) signaling, by catalyzing the extracellular release of palmitate- and cholesterol-modified Hh ligands from producing cells. Disp function requires Furin-mediated proteolytic cleavage of its extracellular domain, but how this activates Disp remains obscure. Here, we employ cryo-electron microscopy to determine atomic structures of human Disp1 (hDisp1), before and after cleavage, and in complex with lipid-modified Sonic hedgehog (Shh) ligand. These structures, together with biochemical data, reveal that proteolytic cleavage opens the extracellular domain of hDisp1, removing steric hindrance to Shh binding. Structure-guided functional experiments demonstrate the role of hDisp1-Shh interactions in ligand release. Our results clarify the mechanisms of hDisp1 activation and Shh morphogen release, and highlight how a unique proteolytic cleavage event enabled acquisition of a protein substrate by a member of a family of small molecule transporters. | |||||||||
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_30956.map.gz | 22.3 MB | EMDB map data format | |
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Header (meta data) | emd-30956-v30.xml emd-30956.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_30956.png | 43.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30956 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30956 | HTTPS FTP |
-Validation report
Summary document | emd_30956_validation.pdf.gz | 460.7 KB | Display | EMDB validaton report |
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Full document | emd_30956_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | emd_30956_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_30956_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30956 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30956 | HTTPS FTP |
-Related structure data
Related structure data | 7e2gMC 7e2hC 7e2iC 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_30956.map.gz / Format: CCP4 / Size: 23.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 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 : hDisp1NNN-3C
Entire | Name: hDisp1NNN-3C |
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Components |
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-Supramolecule #1: hDisp1NNN-3C
Supramolecule | Name: hDisp1NNN-3C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Protein dispatched homolog 1,Protein dispatched homolog 1
Macromolecule | Name: Protein dispatched homolog 1,Protein dispatched homolog 1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 169.906828 KDa |
Recombinant expression | Organism: Mammalian expression vector Flag-EGFP-MCS-pcDNA3.1 (others) |
Sequence | String: MAMSNGNNDF VVLSNSSIAT SAANPSPLTP CDGDHAAQQL TPKEATRTKV SPNGCLQLNG TVKSSFLPLD NQRMPQMLPQ CCHPCPYHH PLTSHSSHQE CHPEAGPAAP SALASCCMQP HSEYSASLCP NHSPVYQTTC CLQPSPSFCL HHPWPDHFQH Q PVQQHIAN ...String: MAMSNGNNDF VVLSNSSIAT SAANPSPLTP CDGDHAAQQL TPKEATRTKV SPNGCLQLNG TVKSSFLPLD NQRMPQMLPQ CCHPCPYHH PLTSHSSHQE CHPEAGPAAP SALASCCMQP HSEYSASLCP NHSPVYQTTC CLQPSPSFCL HHPWPDHFQH Q PVQQHIAN IRPSRPFKLP KSYAALIADW PVVVLGMCTM FIVVCALVGV LVPELPDFSD PLLGFEPRGT AIGQRLVTWN NM VKNTGYK ATLANYPFKY ADEQASSLEV LFQGPGSEVD WNFHKDSFFC DVPSDRYSRV VFTSSGGETL WNLPAIKSMC NVD NSRIRS HPQFGDLCQR TTAASCCPSW TLGNYIAILN NRSSCQKIVE RDVSHTLKLL RTCAKHYQNG TLGPDCWDMA ARRK DQLKC TNVPRKCTKY NAVYQILHYL VDKDFMTPKT ADYATPALKY SMLFSPTEKG ESMMNIYLDN FENWNSSDGV TTITG IEFG IKHSLFQDYL LMDTVYPAIA IVIVLLVMCV YTKSMFITLM TMFAIISSLI VSYFLYRVVF HFEFFPFMNL TALIIL VGI GANNAFVLCD VWNYTKFDKP HAETSETVSI TLQHAALSMF VTSFTTAAAF YANYVSNITA IRCFGVYAGT AILVNYV LM VTWLPAVVVL HERYLLNIFT CFKKPQQQIY DNKSCWTVAC QKCHKVLFAI SEASRIFFEK VLPCIVIKFR YLWLFWFL A LTVGGAYIVC INPKMKLPSL ELSEFQVFRS SHPFERYDAE YKKLFMFERV HHGEELHMPI TVIWGVSPED NGNPLNPKS KGKLTLDSSF NIASPASQAW ILHFCQKLRN QTFFYQTDEQ DFTSCFIETF KQWMENQDCD EPALYPCCSH WSFPYKQEIF ELCIKRAIM ELERSTGYHL DSKTPGPRFD INDTIRAVVL EFQSTYLFTL AYEKMHQFYK EVDSWISSEL SSAPEGLSNG W FVSNLEFY DLQDSLSDGT LIAMGLSVAV AFSVMLLTTW NIIISLYAII SIAGTIFVTV GSLVLLGWEL NVLESVTISV AV GLSVNFA VHYGVAYRLA PDPDREGKVI FSLSRVGSAM AMAALTTFVA GAMMMPSTVL AYTQLGTFMM LIMCISWAFA TFF FQCMCR CLGPQGTCGQ IPLPKKLQCS AFSHALSTSP SDKGQSKTHT INAYHLDPRG PKSELEHEFY ELEPLASHSC TAPE KTTYE ETHICSEFFN SQAKNLGMPV HAAYNSELSK STESDAGSAL LQPPLEQHTV CHFFSLNQRC SCPDAYKHLN YGPHS CQQM GDCLCHQCSP TTSSFVQIQN GVAPLKATHQ AVEGFVHPIT HIHHCPCLQG RVKPAGMQNS LPRNFFLHPV QHIQAQ EKI GKTNVHSLQR SIEEHLPKMA EPSSFVCRST GSLLKTCCDP ENKQRELCKN RDVSNLESSG GTENKAGGKV ELSLSQT DA SVNSEHFNQN EPKVLFNHLM GEAGCRSCPN NSQSCGRIVR VKCNSVDCQM PNMEANVPAV LTHSELSGES LLIKTL |
-Macromolecule #2: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 11 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / 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
Concentration | 7.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159333 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |