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- PDB-7rpk: Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rpk | ||||||||||||||||||
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Title | Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog | ||||||||||||||||||
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![]() | MEMBRANE PROTEIN / RND transporter / Hedgehog binding / Sterol sensing domain / sodium binding | ||||||||||||||||||
Function / homology | ![]() forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis ...forebrain regionalization / cell proliferation in external granule layer / zona limitans intrathalamica formation / positive regulation of neurotrophin production / positive regulation of photoreceptor cell differentiation / fungiform papilla development / Release of Hh-Np from the secreting cell / digestive tract mesoderm development / epithelial-mesenchymal signaling involved in prostate gland development / fungiform papilla morphogenesis / ventral spinal cord interneuron specification / tongue morphogenesis / respiratory tube development / Ligand-receptor interactions / patched ligand maturation / Activation of SMO / mesenchymal-epithelial cell signaling involved in prostate gland development / positive regulation of oligodendrocyte progenitor proliferation / trachea development / positive regulation of skeletal muscle cell proliferation / anatomical structure formation involved in morphogenesis / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / polarity specification of anterior/posterior axis / trunk neural crest cell migration / hindgut morphogenesis / striated muscle tissue development / negative regulation of alpha-beta T cell differentiation / regulation of glial cell proliferation / regulation of prostatic bud formation / metanephric mesenchymal cell proliferation involved in metanephros development / positive regulation of penile erection / formation of anatomical boundary / lung epithelium development / positive regulation of striated muscle cell differentiation / neural tube formation / trachea morphogenesis / myotube differentiation / regulation of epithelial cell proliferation involved in prostate gland development / cholesterol-protein transferase activity / bud outgrowth involved in lung branching / diaphragm development / telencephalon regionalization / epithelial-mesenchymal cell signaling / laminin-1 binding / vasculogenesis involved in coronary vascular morphogenesis / Hedgehog ligand biogenesis / salivary gland cavitation / negative regulation of cholesterol efflux / determination of left/right asymmetry in lateral mesoderm / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / cell development / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / intermediate filament organization / cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / embryonic skeletal system development / male genitalia morphogenesis / limb bud formation / lung lobe morphogenesis / prostate gland development / skeletal muscle fiber differentiation / establishment of epithelial cell polarity / fungiform papilla formation / thalamus development / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / somite development / patched binding / epithelial cell proliferation involved in salivary gland morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / animal organ formation / ectoderm development / neuron fate commitment / branching involved in prostate gland morphogenesis / stem cell development / dorsal/ventral neural tube patterning / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / negative thymic T cell selection / skeletal muscle cell proliferation / lymphoid progenitor cell differentiation / mesenchymal cell proliferation / positive regulation of immature T cell proliferation in thymus Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
![]() | Asarnow, D. / Wang, Q. / Ding, K. / Cheng, Y. / Beachy, P.A. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Dispatched uses Na flux to power release of lipid-modified Hedgehog. Authors: Qianqian Wang / Daniel E Asarnow / Ke Ding / Randall K Mann / Jason Hatakeyama / Yunxiao Zhang / Yong Ma / Yifan Cheng / Philip A Beachy / ![]() ![]() Abstract: The Dispatched protein, which is related to the NPC1 and PTCH1 cholesterol transporters and to H-driven transporters of the RND family, enables tissue-patterning activity of the lipid-modified ...The Dispatched protein, which is related to the NPC1 and PTCH1 cholesterol transporters and to H-driven transporters of the RND family, enables tissue-patterning activity of the lipid-modified Hedgehog protein by releasing it from tightly -localized sites of embryonic expression. Here we determine a cryo-electron microscopy structure of the mouse protein Dispatched homologue 1 (DISP1), revealing three Na ions coordinated within a channel that traverses its transmembrane domain. We find that the rate of Hedgehog export is dependent on the Na gradient across the plasma membrane. The transmembrane channel and Na binding are disrupted in DISP1-NNN, a variant with asparagine substitutions for three intramembrane aspartate residues that each coordinate and neutralize the charge of one of the three Na ions. DISP1-NNN and variants that disrupt single Na sites retain binding to, but are impaired in export of the lipid-modified Hedgehog protein to the SCUBE2 acceptor. Interaction of the amino-terminal signalling domain of the Sonic hedgehog protein (ShhN) with DISP1 occurs via an extensive buried surface area and contacts with an extended furin-cleaved DISP1 arm. Variability analysis reveals that ShhN binding is restricted to one extreme of a continuous series of DISP1 conformations. The bound and unbound DISP1 conformations display distinct Na-site occupancies, which suggests a mechanism by which transmembrane Na flux may power extraction of the lipid-linked Hedgehog signal from the membrane. Na-coordinating residues in DISP1 are conserved in PTCH1 and other metazoan RND family members, suggesting that Na flux powers their conformationally driven activities. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.2 KB | Display | ![]() |
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PDB format | ![]() | 192.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 66.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24617MC ![]() 7rphC ![]() 7rpiC ![]() 7rpjC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AH
#1: Protein | Mass: 152071.141 Da / Num. of mol.: 1 / Fragment: UNP residues 172-1521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 18732.090 Da / Num. of mol.: 1 / Fragment: UNP residues 26-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 1 types, 5 molecules ![](data/chem/img/NAG.gif)
#7: Sugar | ChemComp-NAG / |
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-Non-polymers , 8 types, 77 molecules ![](data/chem/img/Y01.gif)
![](data/chem/img/AV0.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/6OE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AV0.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/6OE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-Y01 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-6OE / ( | #8: Chemical | #9: Chemical | ChemComp-ZN / | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Dispatched protein complexed with Sonic hedgehog 26-189 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.15191493 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.56 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K Details: Wait time 20 seconds, blot time 4 seconds, blotting force 0 |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS Details: Automated data collection in SerialEM using 3x3 image shift pattern (one shot per hole), using beam tilt compensation. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 59880 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 66.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1687 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1406648 | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204786 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | B value: 69.9 / Protocol: FLEXIBLE FIT / Space: REAL |