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- PDB-6xt9: Subunits BBS 1,4,8,9,18 of the human BBSome complex -

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Basic information

Entry
Database: PDB / ID: 6xt9
TitleSubunits BBS 1,4,8,9,18 of the human BBSome complex
Components
  • BBSome-interacting protein 1
  • Bardet-Biedl syndrome 1 protein
  • Bardet-Biedl syndrome 4 protein
  • Protein PTHB1
  • Tetratricopeptide repeat domain 8 isoform 2
KeywordsPROTEIN TRANSPORT / ciliary transport / Arl6 effector / adaptor protein / complex
Function / homology
Function and homology information


regulation of non-motile cilium assembly / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / BBSome / photoreceptor cell morphogenesis / retinal rod cell development / sperm flagellum assembly / negative regulation of appetite by leptin-mediated signaling pathway / photoreceptor cell outer segment organization / smoothened binding ...regulation of non-motile cilium assembly / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / BBSome / photoreceptor cell morphogenesis / retinal rod cell development / sperm flagellum assembly / negative regulation of appetite by leptin-mediated signaling pathway / photoreceptor cell outer segment organization / smoothened binding / olfactory behavior / regulation of cilium beat frequency involved in ciliary motility / microtubule anchoring at centrosome / protein localization to organelle / sensory processing / ciliary transition zone / photoreceptor connecting cilium / patched binding / negative regulation of actin filament polymerization / BBSome-mediated cargo-targeting to cilium / ventricular system development / positive regulation of cilium assembly / sensory perception / striatum development / melanosome transport / protein localization to cilium / maintenance of protein location in nucleus / positive regulation of multicellular organism growth / photoreceptor cell maintenance / regulation of stress fiber assembly / non-motile cilium assembly / Golgi to plasma membrane protein transport / brain morphogenesis / negative regulation of systemic arterial blood pressure / retina homeostasis / hormone metabolic process / fertilization / cartilage development / non-motile cilium / protein localization to centrosome / centrosome cycle / neural precursor cell proliferation / eating behavior / fat pad development / motile cilium / erythrocyte homeostasis / ciliary membrane / heart looping / fat cell differentiation / face development / pericentriolar material / adult behavior / dendrite development / B cell homeostasis / dynactin binding / regulation of lipid metabolic process / mitotic cytokinesis / axoneme / social behavior / cilium assembly / anatomical structure morphogenesis / spermatid development / photoreceptor outer segment / alpha-tubulin binding / intracellular transport / beta-tubulin binding / photoreceptor inner segment / visual perception / centriole / response to endoplasmic reticulum stress / regulation of cytokinesis / neural tube closure / hippocampus development / phosphoprotein binding / cerebral cortex development / lipid metabolic process / centriolar satellite / microtubule cytoskeleton organization / Wnt signaling pathway / fibrillar center / neuron migration / sensory perception of smell / protein transport / retina development in camera-type eye / protein-macromolecule adaptor activity / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / cilium / ciliary basal body / negative regulation of gene expression / centrosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / : / Cilia BBSome complex subunit 10 / Bardet-Biedl syndrome 1 protein, GAE domain / Parathyroid hormone-responsive B1 / PTHB1, N-terminal domain / PTHB1, C-terminal domain / : / : ...Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / : / Cilia BBSome complex subunit 10 / Bardet-Biedl syndrome 1 protein, GAE domain / 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 / Tetratricopeptide repeat / TPR 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
Similarity search - Domain/homology
Tetratricopeptide repeat protein 8 / BBSome-interacting protein 1 / Protein PTHB1 / BBSome complex member BBS1 / BBSome complex member BBS4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKlink, B.U. / Raunser, S. / Gatsogiannis, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Elife / Year: 2020
Title: Structure of the human BBSome core complex.
Authors: Björn Udo Klink / Christos Gatsogiannis / Oliver Hofnagel / Alfred Wittinghofer / Stefan Raunser /
Abstract: The BBSome is a heterooctameric protein complex that plays a central role in primary cilia homeostasis. Its malfunction causes the severe ciliopathy Bardet-Biedl syndrome (BBS). The complex acts as a ...The BBSome is a heterooctameric protein complex that plays a central role in primary cilia homeostasis. Its malfunction causes the severe ciliopathy Bardet-Biedl syndrome (BBS). The complex acts as a cargo adapter that recognizes signaling proteins such as GPCRs and links them to the intraflagellar transport machinery. The underlying mechanism is poorly understood. Here we present a high-resolution cryo-EM structure of a human heterohexameric core subcomplex of the BBSome. The structure reveals the architecture of the complex in atomic detail. It explains how the subunits interact with each other and how disease-causing mutations hamper this interaction. The complex adopts a conformation that is open for binding to membrane-associated GTPase Arl6 and a large positively charged patch likely strengthens the interaction with the membrane. A prominent negatively charged cleft at the center of the complex is likely involved in binding of positively charged signaling sequences of cargo proteins.
History
DepositionJan 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Category: em_imaging_optics / Item: _em_imaging_optics.phase_plate
Revision 1.2May 22, 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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Assembly

Deposited unit
A: Bardet-Biedl syndrome 1 protein
D: Bardet-Biedl syndrome 4 protein
H: Tetratricopeptide repeat domain 8 isoform 2
I: Protein PTHB1
J: BBSome-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)298,1405
Polymers298,1405
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25700 Å2
ΔGint-152 kcal/mol
Surface area100550 Å2

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Components

#1: Protein Bardet-Biedl syndrome 1 protein / BBS2-like protein 2


Mass: 65159.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBS1, BBS2L2 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NFJ9
#2: Protein Bardet-Biedl syndrome 4 protein


Mass: 59463.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBS4 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96RK4
#3: Protein Tetratricopeptide repeat domain 8 isoform 2 / Tetratricopeptide repeat protein 8


Mass: 58702.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC8 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0C4DGY3
#4: Protein Protein PTHB1 / Bardet-Biedl syndrome 9 protein / Parathyroid hormone-responsive B1 gene protein


Mass: 99383.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBS9, PTHB1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q3SYG4
#5: Protein BBSome-interacting protein 1 / BBSome-interacting protein of 10 kDa


Mass: 15430.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BBIP1, BBIP10, NCRNA00081 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8MTZ0

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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 core complex / Type: COMPLEX
Details: BBSome core complex containing BBS1,4, 8, 9 and 18. BBS5 was also present in the sample preparation, but was only visible in a subset of particles (see related entry)
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: Hi5 / Plasmid: ACEMBL
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMTRIS-HCL1
2150 mMNaCl1
30.1 mMTCEP1
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was cross linked with 0.5% glutaraldehyde
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 K
Details: double blot with 2 minutes incubation after first sample application

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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: OTHER
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 300 nm / Calibrated defocus max: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 15 sec. / Electron dose: 67 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 15266
EM imaging opticsEnergyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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Processing

EM software
IDNameVersionCategoryDetails
1SPHIRE1.2-1.3particle selectionCryolo
2EPUimage acquisition
3SPHIREimage acquisitionTransphire used to aid data collection
5CTFFIND4.1.10CTF correction
11SPHIRE1.2-1.3initial Euler assignment
12SPHIRE1.2-1.3final Euler assignmentMeridien
13SPHIRE1.2-1.3classificationISAC
14SPHIRE1.2-1.33D reconstructionMeridien
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2831329
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 862114 / Symmetry type: POINT

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