+Open data
-Basic information
Entry | Database: PDB / ID: 6vbu | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the bovine BBSome complex | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / Cilia / ciliopathy / complex / membrane-protein 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 / renal tubule development / BBSome / 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 / renal tubule development / BBSome / 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 / non-motile cilium assembly / establishment of epithelial cell apical/basal polarity / protein localization to cilium / phosphatidylinositol-3-phosphate binding / regulation of stress fiber assembly / non-motile cilium / motile cilium / centrosome cycle / ciliary membrane / pericentriolar material / fat cell differentiation / axoneme / centriolar satellite / cilium assembly / intracellular transport / ciliary basal body / protein localization to plasma membrane / axon guidance / multicellular organism growth / cilium / regulation of protein localization / protein localization / sensory perception of smell / protein transport / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / neuron projection / centrosome / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Singh, S.K. / Gui, M. / Koh, F. / Yip, M.C.J. / Brown, A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Elife / Year: 2020 Title: Structure and activation mechanism of the BBSome membrane protein trafficking complex. Authors: Sandeep K Singh / Miao Gui / Fujiet Koh / Matthew Cj Yip / Alan Brown / Abstract: Bardet-Biedl syndrome (BBS) is a currently incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS ...Bardet-Biedl syndrome (BBS) is a currently incurable ciliopathy caused by the failure to correctly establish or maintain cilia-dependent signaling pathways. Eight proteins associated with BBS assemble into the BBSome, a key regulator of the ciliary membrane proteome. We report the electron cryomicroscopy (cryo-EM) structures of the native bovine BBSome in inactive and active states at 3.1 and 3.5 Å resolution, respectively. In the active state, the BBSome is bound to an Arf-family GTPase (ARL6/BBS3) that recruits the BBSome to ciliary membranes. ARL6 recognizes a composite binding site formed by BBS1 and BBS7 that is occluded in the inactive state. Activation requires an unexpected swiveling of the β-propeller domain of BBS1, the subunit most frequently implicated in substrate recognition, which widens a central cavity of the BBSome. Structural mapping of disease-causing mutations suggests that pathogenesis results from folding defects and the disruption of autoinhibition and activation. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vbu.cif.gz | 678.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vbu.ent.gz | 544.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vbu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6vbu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6vbu_validation.xml.gz | 113.2 KB | Display | |
Data in CIF | 6vbu_validation.cif.gz | 170.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/6vbu ftp://data.pdbj.org/pub/pdb/validation_reports/vb/6vbu | HTTPS FTP |
-Related structure data
Related structure data | 21144MC 6vbvC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Bardet-Biedl syndrome ... , 7 types, 7 molecules 0245789
#1: Protein | Mass: 8070.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: G3N2W1 |
---|---|
#3: Protein | Mass: 79911.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: Q32L13 |
#4: Protein | Mass: 58289.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: Q1JQ97 |
#5: Protein | Mass: 38880.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: A6QLF9 |
#6: Protein | Mass: 80471.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: F1MB52 |
#7: Protein | Mass: 56686.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: F1N4X0 |
#8: Protein | Mass: 99230.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: E1BHJ5 |
-Protein / Non-polymers , 2 types, 3 molecules 1
#2: Protein | Mass: 64939.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Eye / Tissue: Retina / References: UniProt: E1BN34 |
---|---|
#9: Chemical |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Bovine BBSome complex / Type: COMPLEX / Details: Native BBSome complex isolated from bovine retina / Entity ID: #1-#8 / Source: NATURAL | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) / Organ: Eye / Tissue: Retina | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: The buffer also contained 36 uM ARL6 and 1 mM GTP. | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: The grids were glow discharged at 15 mA for 30 s with a PELCO easiGlow Glow Discharge Cleaning System. Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: Grids were blotted for 2 s with a -2 offset. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 9408 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152942 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 43.6 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient Details: During refinement, the resolution limit was set to 3.1 Angstrom. Secondary structure, Ramachandran and rotamer restraints were applied during refinement. |