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- PDB-6vnw: Cryo-EM structure of apo-BBSome -

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Basic information

Entry
Database: PDB / ID: 6vnw
TitleCryo-EM structure of apo-BBSome
Components
  • (Bardet-Biedl syndrome ...Bardet–Biedl syndrome) x 6
  • BBS1 domain-containing protein
  • Tetratricopeptide repeat domain 8
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


primary palate development / regulation of non-motile cilium assembly / negative regulation of appetite by leptin-mediated signaling pathway / multi-ciliated epithelial cell differentiation / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium / protein localization to photoreceptor outer segment / regulation of cilium beat frequency involved in ciliary motility / BBSome ...primary palate development / regulation of non-motile cilium assembly / negative regulation of appetite by leptin-mediated signaling pathway / multi-ciliated epithelial cell differentiation / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium / protein localization to photoreceptor outer segment / regulation of cilium beat frequency involved in ciliary motility / BBSome / camera-type eye photoreceptor cell differentiation / photoreceptor cell morphogenesis / retinal rod cell development / ventricular system development / ciliary transition zone / establishment of planar polarity / smoothened binding / olfactory behavior / microtubule anchoring at centrosome / positive regulation of cilium assembly / olfactory bulb development / neural precursor cell proliferation / photoreceptor connecting cilium / negative regulation of systemic arterial blood pressure / inner ear receptor cell stereocilium organization / striatum development / non-motile cilium / patched binding / protein localization to cilium / intracellular transport / non-motile cilium assembly / maintenance of protein location in nucleus / cellular lipid metabolic process / hormone metabolic process / eye development / negative regulation of actin filament polymerization / brain morphogenesis / eating behavior / establishment of epithelial cell apical/basal polarity / motile cilium / positive regulation of multicellular organism growth / photoreceptor cell maintenance / phosphatidylinositol-3-phosphate binding / limb development / smoothened signaling pathway / sensory perception of smell / ciliary membrane / fertilization / centrosome cycle / fat pad development / beta-tubulin binding / ciliary basal body / dynactin binding / adult behavior / protein localization to centrosome / photoreceptor outer segment / regulation of stress fiber assembly / cartilage development / spermatid development / fat cell differentiation / negative regulation of GTPase activity / face development / pericentriolar material / alpha-tubulin binding / microtubule motor activity / dendrite development / centriolar satellite / cilium assembly / social behavior / RNA polymerase II repressing transcription factor binding / axoneme / mitotic cytokinesis / cilium / centriole / photoreceptor inner segment / protein localization to plasma membrane / microtubule organizing center / cerebral cortex development / hippocampus development / regulation of protein localization / protein localization / regulation of cytokinesis / neuron migration / neural tube closure / phosphoprotein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton organization / protein transport / regulation of lipid metabolic process / multicellular organism growth / axon guidance / brain development / retina homeostasis / heart development / negative regulation of gene expression / centrosome / neuron projection / regulation of transcription by RNA polymerase II / membrane / nucleus
Tetratricopeptide repeat-containing domain / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 1 protein / Tetratricopeptide repeat protein 8 / DM16 repeat / Ciliary BBSome complex subunit 2, C-terminal domain / PTHB1, N-terminal domain / Parathyroid hormone-responsive B1 / Ciliary BBSome complex subunit 2, middle region / Tetratricopeptide repeat ...Tetratricopeptide repeat-containing domain / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 1 protein / Tetratricopeptide repeat protein 8 / DM16 repeat / Ciliary BBSome complex subunit 2, C-terminal domain / PTHB1, N-terminal domain / Parathyroid hormone-responsive B1 / Ciliary BBSome complex subunit 2, middle region / Tetratricopeptide repeat / Ciliary BBSome complex subunit 2, N-terminal / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / PTHB1, C-terminal domain / Bardet-Biedl syndrome 1, N-terminal / Bardet-Biedl syndrome 2 protein / WD40-repeat-containing domain superfamily / Bardet-Biedl syndrome 5 protein / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Cilia BBSome complex subunit 10
Bardet-Biedl syndrome 5 protein homolog / Uncharacterized protein / BBS1 domain-containing protein / Bardet-Biedl syndrome 7 protein homolog / Tetratricopeptide repeat domain 8 / Uncharacterized protein / Bardet-Biedl syndrome 4 protein homolog / Bardet-Biedl syndrome 2 protein homolog
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYang, S. / Walz, T. / Nachury, M. / Chou, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM089933 United States
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
H: Bardet-Biedl syndrome 18 protein
B: Bardet-Biedl syndrome 2 protein homolog
E: Bardet-Biedl syndrome 4 protein homolog
G: Bardet-Biedl syndrome 5 protein homolog
C: Bardet-Biedl syndrome 7 protein homolog
F: Tetratricopeptide repeat domain 8
I: Bardet-Biedl syndrome 9
D: BBS1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)486,4808
Polymers486,4808
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Bardet-Biedl syndrome ... , 6 types, 6 molecules HBEGCI

#1: Protein Bardet-Biedl syndrome 18 protein / Bardet–Biedl syndrome


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
#2: Protein Bardet-Biedl syndrome 2 protein homolog / Bardet–Biedl syndrome


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 Bardet-Biedl syndrome 4 protein homolog / Bardet–Biedl syndrome


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 Bardet-Biedl syndrome 5 protein homolog / Bardet–Biedl syndrome


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 Bardet-Biedl syndrome 7 protein homolog / Bardet–Biedl syndrome


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 Bardet-Biedl syndrome 9 / Bardet–Biedl syndrome


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

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Protein , 2 types, 2 molecules FD

#6: Protein Tetratricopeptide repeat domain 8


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
#8: Protein BBS1 domain-containing 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BBSome complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaClSodium chloride1
30.7 mMMagnesium chlorideMgCl21
41 mMDTTC4H10O2S21
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Wait time 20s, blot force -2, blot time 3.5s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 560777 / Symmetry type: POINT

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