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- PDB-6voa: Cryo-EM structure of the BBSome-ARL6 complex -

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Basic information

Entry
Database: PDB / ID: 6voa
TitleCryo-EM structure of the BBSome-ARL6 complex
Components
  • (Bardet-Biedl syndrome ...Bardet–Biedl syndrome) x 6
  • ADP-ribosylation factor-like protein 6
  • BBS1 domain-containing protein
  • Tetratricopeptide repeat domain 8
KeywordsPROTEIN TRANSPORT / Cilia / Bardet-Biedl Syndrome
Function / homology
Function and homology information


BBSome binding / protein transport from ciliary membrane to plasma membrane / protein localization to non-motile cilium / primary palate development / regulation of non-motile cilium assembly / multi-ciliated epithelial cell differentiation / negative regulation of appetite by leptin-mediated signaling pathway / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium ...BBSome binding / protein transport from ciliary membrane to plasma membrane / protein localization to non-motile cilium / primary palate development / regulation of non-motile cilium assembly / multi-ciliated epithelial cell differentiation / negative regulation of appetite by leptin-mediated signaling pathway / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium / axonemal microtubule / 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 / retina layer formation / smoothened binding / establishment of planar polarity / olfactory behavior / microtubule anchoring at centrosome / positive regulation of cilium assembly / olfactory bulb development / photoreceptor connecting cilium / negative regulation of systemic arterial blood pressure / inner ear receptor cell stereocilium organization / neural precursor cell proliferation / patched binding / striatum development / non-motile cilium / protein localization to cilium / cellular lipid metabolic process / non-motile cilium assembly / maintenance of protein location in nucleus / membrane coat / intracellular transport / negative regulation of actin filament polymerization / hormone metabolic process / brain morphogenesis / eye development / establishment of epithelial cell apical/basal polarity / eating behavior / motile cilium / positive regulation of multicellular organism growth / photoreceptor cell maintenance / centrosome cycle / limb development / phosphatidylinositol-3-phosphate binding / smoothened signaling pathway / regulation of smoothened signaling pathway / protein targeting to membrane / ciliary membrane / fertilization / sensory perception of smell / beta-tubulin binding / fat pad development / fat cell differentiation / dynactin binding / protein localization to centrosome / adult behavior / photoreceptor outer segment / cartilage development / spermatid development / regulation of stress fiber assembly / face development / ciliary basal body / protein polymerization / negative regulation of GTPase activity / pericentriolar material / alpha-tubulin binding / microtubule motor activity / centriolar satellite / cilium assembly / social behavior / dendrite development / RNA polymerase II repressing transcription factor binding / axoneme / mitotic cytokinesis / cilium / centriole / protein localization to plasma membrane / photoreceptor inner segment / microtubule organizing center / vesicle-mediated transport / cerebral cortex development / hippocampus development / protein localization / regulation of cytokinesis / regulation of protein localization / phospholipid binding / neuron migration / neural tube closure / phosphoprotein binding / intracellular protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton organization / protein transport
Tetratricopeptide-like helical domain superfamily / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / Tetratricopeptide repeat-containing domain / DM16 repeat / Bardet-Biedl syndrome 2 protein / Tetratricopeptide repeat / Parathyroid hormone-responsive B1 / P-loop containing nucleoside triphosphate hydrolase / PTHB1, N-terminal domain / PTHB1, C-terminal domain ...Tetratricopeptide-like helical domain superfamily / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / Tetratricopeptide repeat-containing domain / DM16 repeat / Bardet-Biedl syndrome 2 protein / Tetratricopeptide repeat / Parathyroid hormone-responsive B1 / P-loop containing nucleoside triphosphate hydrolase / PTHB1, N-terminal domain / PTHB1, C-terminal domain / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 1 protein / Tetratricopeptide repeat protein 8 / Ciliary BBSome complex subunit 2, C-terminal domain / Ciliary BBSome complex subunit 2, middle region / Ciliary BBSome complex subunit 2, N-terminal / Cilia BBSome complex subunit 10 / Bardet-Biedl syndrome 1, N-terminal / Small GTP-binding protein domain / Bardet-Biedl syndrome 5 protein / Small GTPase superfamily, ARF/SAR type / WD40-repeat-containing domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / ADP-ribosylation factor-like protein 6 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Bardet-Biedl syndrome 5 protein homolog / Uncharacterized protein / BBS1 domain-containing protein / Bardet-Biedl syndrome 7 protein homolog / Tetratricopeptide repeat domain 8 / Uncharacterized protein / ADP-ribosylation factor-like protein 6 / Bardet-Biedl syndrome 4 protein homolog / Bardet-Biedl syndrome 2 protein homolog
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsYang, S. / Walz, T. / Nachury, M.V.
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 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release

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Structure visualization

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Structure viewerMolecule:
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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
A: ADP-ribosylation factor-like protein 6
D: BBS1 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)507,5669
Polymers507,5669
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) / 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) / 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) / 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) / 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) / 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) / References: UniProt: E1BHJ5

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Protein , 3 types, 3 molecules FAD

#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) / References: UniProt: F1N4X0
#8: Protein ADP-ribosylation factor-like protein 6


Mass: 21086.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARL6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0IIM2
#9: 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) / 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

Component
IDNameTypeEntity IDParent-IDSource
1BBSome complex with ARL6 boundCOMPLEX#1-#90MULTIPLE SOURCES
2Bardet-Biedl syndrome 18 protein, BBS18, Bardet-Biedl syndrome 2 protein homolog, Bardet-Biedl syndrome 7 protein homolog, BBS1 domain-containing protein, Bardet-Biedl syndrome 4 protein homolog, Tetratricopeptide repeat domain 8, Bardet-Biedl syndrome 5 protein homolog, Bardet-Biedl syndrome 9Bardet–Biedl syndromeCOMPLEX#1-#7, #91NATURAL
3ADP-ribosylation factor-like protein 6COMPLEX#81RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (cattle)9913
23Bos taurus (cattle)9913
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1175.2GATAN K2 SUMMIT (4k x 4k)
2151.44GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Image processingDetails: For final refinement, particles were combined from data of both K2 and K3 detector.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546186 / Symmetry type: POINT

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