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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 ...) x 6
  • BBS1 domain-containing protein
  • Tetratricopeptide repeat domain 8
KeywordsPROTEIN 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 / BBSome / renal tubule development / 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 / BBSome / renal tubule development / 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 / establishment of epithelial cell apical/basal polarity / protein localization to cilium / non-motile cilium assembly / phosphatidylinositol-3-phosphate binding / regulation of stress fiber assembly / non-motile cilium / centrosome cycle / motile cilium / ciliary membrane / pericentriolar material / fat cell differentiation / axoneme / cilium assembly / intracellular transport / axon guidance / protein localization to plasma membrane / multicellular organism growth / centriolar satellite / fibrillar center / sensory perception of smell / intracellular protein localization / protein transport / regulation of protein localization / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / neuron projection / ciliary basal body / cilium / centrosome / membrane / cytoplasm
Similarity search - Function
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 / : / : / : / : / : ...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 / BBS2 GAE domain / Ciliary BBSome complex subunit 2, middle region / BBS7 hairpin / BBS2 platform domain / BBS2 C-terminal helix bundle / BBS2 hairpin / BBS7 GAE domain / BBS7 platform domain / : / BBS7 beta-propeller / 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 / Bardet-Biedl syndrome 1 protein, GAE domain / 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-terminal / PTHB1 GAE domain / PTHB1 platform domain / PTHB1 hairpin / PTHB1 C-terminal helix bundle / Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 1, N-terminal / Ciliary BBSome complex subunit 1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
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 / BBSome complex member BBS4 / Bardet-Biedl syndrome 2 protein homolog
Similarity search - Component
Biological speciesBos taurus (domestic 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.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 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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  • Deposited structure unit
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  • EMDB-21251
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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
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 (domestic cattle) / Tissue: retina / 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 (domestic cattle) / Tissue: retina / 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 (domestic cattle) / Tissue: retina / 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 (domestic cattle) / Tissue: retina / 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 (domestic cattle) / Tissue: retina / 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 (domestic 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 (domestic 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 (domestic 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: all / Source: NATURAL
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle) / Tissue: retina
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
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 FIELD
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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