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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 ...) 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 / 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 ...BBSome binding / 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 / axonemal microtubule / inner ear receptor cell stereocilium organization / patched binding / olfactory bulb development / membrane coat / 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 / protein targeting to membrane / centrosome cycle / ciliary membrane / pericentriolar material / fat cell differentiation / axoneme / centriolar satellite / protein polymerization / cilium assembly / intracellular transport / vesicle-mediated transport / ciliary basal body / protein localization to plasma membrane / axon guidance / intracellular protein transport / protein localization / multicellular organism growth / phospholipid binding / 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 / GTPase activity / centrosome / GTP binding / membrane / cytoplasm
Similarity search - Function
ADP-ribosylation factor-like protein 6 / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 2 protein / Ciliary BBSome complex subunit 2, C-terminal domain / Ciliary BBSome complex subunit 2, middle region / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, C-terminal / Ciliary BBSome complex subunit 2, middle region / Bardet-Biedl syndrome 5 protein ...ADP-ribosylation factor-like protein 6 / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 2 protein / Ciliary BBSome complex subunit 2, C-terminal domain / Ciliary BBSome complex subunit 2, middle region / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, C-terminal / Ciliary BBSome complex subunit 2, middle region / Bardet-Biedl syndrome 5 protein / DM16 repeat / Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / Bardet-Biedl syndrome 5 protein / Cilia BBSome complex subunit 10 / Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc. / Parathyroid hormone-responsive B1 / PTHB1, N-terminal domain / PTHB1, C-terminal domain / PTHB1 N-terminus / PTHB1 C-terminus / Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 1, N-terminal / Ciliary BBSome complex subunit 1 / TPR repeat / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bardet-Biedl syndrome 5 protein homolog / Bardet-Biedl syndrome 9 / Bardet-Biedl syndrome 1 / Bardet-Biedl syndrome 7 protein homolog / Tetratricopeptide repeat domain 8 / BBSome interacting protein 1 / ADP-ribosylation factor-like protein 6 / Bardet-Biedl syndrome 4 protein homolog / Bardet-Biedl syndrome 2 protein homolog
Similarity search - Component
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.
History
DepositionJan 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • EMDB-21259
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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
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


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


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


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


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


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


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 boundCOMPLEXall0MULTIPLE 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 9COMPLEX#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 FIELD
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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