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Yorodumi- PDB-7v6y: Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v6y | |||||||||||||||
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Title | Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed with dataset of 7dzq) | |||||||||||||||
Components | Protein patched homolog 1,Protein patched homolog 1 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / Caveolae / Hedgehog signaling / Lipid nanodisc / Patched / Ptc1 dimer | |||||||||||||||
Function / homology | Function and homology information Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding ...Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding / hindlimb morphogenesis / Hedgehog 'on' state / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / Hedgehog 'off' state / somite development / patched binding / negative regulation of cell division / cellular response to cholesterol / dorsal/ventral neural tube patterning / smooth muscle tissue development / pattern specification process / pharyngeal system development / mammary gland epithelial cell differentiation / mammary gland duct morphogenesis / mammary gland development / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / dorsal/ventral pattern formation / regulation of growth / embryonic limb morphogenesis / negative regulation of multicellular organism growth / positive regulation of cholesterol efflux / branching involved in ureteric bud morphogenesis / cholesterol binding / negative regulation of osteoblast differentiation / positive regulation of epidermal cell differentiation / regulation of mitotic cell cycle / dendritic growth cone / keratinocyte proliferation / cyclin binding / spermatid development / negative regulation of keratinocyte proliferation / epidermis development / embryonic organ development / axonal growth cone / heart morphogenesis / response to retinoic acid / negative regulation of stem cell proliferation / response to mechanical stimulus / negative regulation of smoothened signaling pathway / epithelial cell proliferation / liver regeneration / stem cell proliferation / caveola / neural tube closure / protein localization to plasma membrane / animal organ morphogenesis / brain development / cilium / protein processing / negative regulation of epithelial cell proliferation / regulation of protein localization / glucose homeostasis / apical part of cell / response to estradiol / heparin binding / regulation of cell population proliferation / midbody / in utero embryonic development / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / zinc ion binding / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Luo, Y. / Zhao, Y. / Qu, Q. / Li, D. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Structure / Year: 2021 Title: Cryo-EM study of patched in lipid nanodisc suggests a structural basis for its clustering in caveolae. Authors: Yitian Luo / Guoyue Wan / Xiang Zhang / Xuan Zhou / Qiuwen Wang / Jialin Fan / Hongmin Cai / Liya Ma / Hailong Wu / Qianhui Qu / Yao Cong / Yun Zhao / Dianfan Li / Abstract: The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of ...The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of downstream regulators. The positive modulator Hh inhibits Ptc1's transporter function by binding to Ptc1 and its co-receptors, which are locally concentrated in invaginated microdomains known as caveolae. Here, we reconstitute the mouse Ptc1 into lipid nanodiscs and determine its structure using single-particle cryoelectron microscopy. The structure is overall similar to those in amphipol and detergents but displays various conformational differences in the transmembrane region. Although most particles show monomers, we observe Ptc1 dimers with distinct interaction patterns and different membrane curvatures, some of which are reminiscent of caveolae. We find that an extramembranous "hand-shake" region rich in hydrophobic and aromatic residues mediates inter-Ptc1 interactions under different membrane curvatures. Our data provide a plausible framework for Ptc1 clustering in the highly curved caveolae. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7v6y.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v6y.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 7v6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v6y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7v6y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7v6y_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7v6y_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/7v6y ftp://data.pdbj.org/pub/pdb/validation_reports/v6/7v6y | HTTPS FTP |
-Related structure data
Related structure data | 31753MC 7v6zC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 121637.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptch1, Ptch / Production host: Homo sapiens (human) / References: UniProt: Q61115 | ||||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | #4: Chemical | ChemComp-5VI / ( | #5: Sugar | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ptc1 in lipid nanodisc / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 160 kDa/nm / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1100 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.23 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1363356 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172299 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 57.04 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MG8 | ||||||||||||||||||||||||||||||||||||||||
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