+Open data
-Basic information
Entry | Database: PDB / ID: 6vnw | ||||||
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Title | Cryo-EM structure of apo-BBSome | ||||||
Components |
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Keywords | PROTEIN TRANSPORT | ||||||
Function / homology | Function and homology information establishment of anatomical structure orientation / BBSome-mediated cargo-targeting to cilium / multi-ciliated epithelial cell differentiation / receptor localization to non-motile cilium / renal tubule development / BBSome / camera-type eye photoreceptor cell differentiation / smoothened binding / establishment of planar polarity / photoreceptor connecting cilium ...establishment of anatomical structure orientation / BBSome-mediated cargo-targeting to cilium / multi-ciliated epithelial cell differentiation / receptor localization to non-motile cilium / renal tubule development / BBSome / camera-type eye photoreceptor cell differentiation / smoothened binding / establishment of planar polarity / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / patched binding / olfactory bulb development / non-motile cilium assembly / phosphatidylinositol-3-phosphate binding / establishment of epithelial cell apical/basal polarity / protein localization to cilium / regulation of stress fiber assembly / non-motile cilium / motile cilium / centrosome cycle / ciliary membrane / pericentriolar material / fat cell differentiation / axoneme / centriolar satellite / cilium assembly / intracellular transport / ciliary basal body / protein localization to plasma membrane / axon guidance / protein localization / multicellular organism growth / cilium / regulation of protein localization / sensory perception of smell / protein transport / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / neuron projection / centrosome / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å | ||||||
Authors | Yang, S. / Walz, T. / Nachury, M. / Chou, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Near-atomic structures of the BBSome reveal the basis for BBSome activation and binding to GPCR cargoes. Authors: Shuang Yang / Kriti Bahl / Hui-Ting Chou / Jonathan Woodsmith / Ulrich Stelzl / Thomas Walz / Maxence V Nachury / Abstract: Dynamic trafficking of G protein-coupled receptors (GPCRs) out of cilia is mediated by the BBSome. In concert with its membrane recruitment factor, the small GTPase ARL6/BBS3, the BBSome ferries ...Dynamic trafficking of G protein-coupled receptors (GPCRs) out of cilia is mediated by the BBSome. In concert with its membrane recruitment factor, the small GTPase ARL6/BBS3, the BBSome ferries GPCRs across the transition zone, a diffusion barrier at the base of cilia. Here, we present the near-atomic structures of the BBSome by itself and in complex with ARL6, and we describe the changes in BBSome conformation induced by ARL6 binding. Modeling the interactions of the BBSome with membranes and the GPCR Smoothened (SMO) reveals that SMO, and likely also other GPCR cargoes, must release their amphipathic helix 8 from the membrane to be recognized by the BBSome. | ||||||
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 | 6vnw.cif.gz | 643.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vnw.ent.gz | 502.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vnw_validation.pdf.gz | 762.7 KB | Display | wwPDB validaton report |
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Full document | 6vnw_full_validation.pdf.gz | 822.8 KB | Display | |
Data in XML | 6vnw_validation.xml.gz | 97.6 KB | Display | |
Data in CIF | 6vnw_validation.cif.gz | 151.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/6vnw ftp://data.pdbj.org/pub/pdb/validation_reports/vn/6vnw | HTTPS FTP |
-Related structure data
Related structure data | 21251MC 6voaC 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
-Bardet-Biedl syndrome ... , 6 types, 6 molecules HBEGCI
#1: Protein | Mass: 8070.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: G3N2W1 |
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#2: Protein | Mass: 79911.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: Q32L13 |
#3: Protein | Mass: 58289.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: Q1JQ97 |
#4: Protein | Mass: 38880.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: A6QLF9 |
#5: Protein | Mass: 80471.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: F1MB52 |
#7: Protein | Mass: 99230.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: E1BHJ5 |
-Protein , 2 types, 2 molecules FD
#6: Protein | Mass: 56686.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: F1N4X0 |
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#8: Protein | Mass: 64939.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: E1BN34 |
-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: BBSome complex / Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) / Tissue: retina | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Wait time 20s, blot force -2, blot time 3.5s |
-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 |
Image recording | Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 560777 / Symmetry type: POINT |