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- EMDB-21251: Cryo-EM structure of apo-BBSome -

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Basic information

Entry
Database: EMDB / ID: EMD-21251
TitleCryo-EM structure of apo-BBSome
Map data
SampleBBSome complex
  • (Bardet-Biedl syndrome ...Bardet–Biedl syndrome) x 6
  • Tetratricopeptide repeat domain 8
  • BBS1 domain-containing protein
Function / homology
Function and homology information


primary palate development / regulation of non-motile cilium assembly / negative regulation of appetite by leptin-mediated signaling pathway / multi-ciliated epithelial cell differentiation / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium / protein localization to photoreceptor outer segment / regulation of cilium beat frequency involved in ciliary motility / BBSome ...primary palate development / regulation of non-motile cilium assembly / negative regulation of appetite by leptin-mediated signaling pathway / multi-ciliated epithelial cell differentiation / renal tubule development / photoreceptor cell outer segment organization / receptor localization to non-motile cilium / 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 / establishment of planar polarity / smoothened binding / olfactory behavior / microtubule anchoring at centrosome / positive regulation of cilium assembly / olfactory bulb development / neural precursor cell proliferation / photoreceptor connecting cilium / negative regulation of systemic arterial blood pressure / inner ear receptor cell stereocilium organization / striatum development / non-motile cilium / patched binding / protein localization to cilium / intracellular transport / non-motile cilium assembly / maintenance of protein location in nucleus / cellular lipid metabolic process / hormone metabolic process / eye development / negative regulation of actin filament polymerization / brain morphogenesis / eating behavior / establishment of epithelial cell apical/basal polarity / motile cilium / positive regulation of multicellular organism growth / photoreceptor cell maintenance / phosphatidylinositol-3-phosphate binding / limb development / smoothened signaling pathway / sensory perception of smell / ciliary membrane / fertilization / centrosome cycle / fat pad development / beta-tubulin binding / ciliary basal body / dynactin binding / adult behavior / protein localization to centrosome / photoreceptor outer segment / regulation of stress fiber assembly / cartilage development / spermatid development / fat cell differentiation / negative regulation of GTPase activity / face development / pericentriolar material / alpha-tubulin binding / microtubule motor activity / dendrite development / centriolar satellite / cilium assembly / social behavior / RNA polymerase II repressing transcription factor binding / axoneme / mitotic cytokinesis / cilium / centriole / photoreceptor inner segment / protein localization to plasma membrane / microtubule organizing center / cerebral cortex development / hippocampus development / regulation of protein localization / protein localization / regulation of cytokinesis / neuron migration / neural tube closure / phosphoprotein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton organization / protein transport / regulation of lipid metabolic process / multicellular organism growth / axon guidance / brain development / retina homeostasis / heart development / negative regulation of gene expression / centrosome / neuron projection / regulation of transcription by RNA polymerase II / membrane / nucleus
Tetratricopeptide repeat-containing domain / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 1 protein / Tetratricopeptide repeat protein 8 / DM16 repeat / Ciliary BBSome complex subunit 2, C-terminal domain / PTHB1, N-terminal domain / Parathyroid hormone-responsive B1 / Ciliary BBSome complex subunit 2, middle region / Tetratricopeptide repeat ...Tetratricopeptide repeat-containing domain / Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 1 protein / Tetratricopeptide repeat protein 8 / DM16 repeat / Ciliary BBSome complex subunit 2, C-terminal domain / PTHB1, N-terminal domain / Parathyroid hormone-responsive B1 / Ciliary BBSome complex subunit 2, middle region / Tetratricopeptide repeat / Ciliary BBSome complex subunit 2, N-terminal / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / PTHB1, C-terminal domain / Bardet-Biedl syndrome 1, N-terminal / Bardet-Biedl syndrome 2 protein / WD40-repeat-containing domain superfamily / Bardet-Biedl syndrome 5 protein / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Cilia BBSome complex subunit 10
Bardet-Biedl syndrome 5 protein homolog / Uncharacterized protein / BBS1 domain-containing protein / Bardet-Biedl syndrome 7 protein homolog / Tetratricopeptide repeat domain 8 / Uncharacterized protein / Bardet-Biedl syndrome 4 protein homolog / Bardet-Biedl syndrome 2 protein homolog
Biological speciesBos taurus (cattle) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYang S / Walz T / Nachury M / Chou H
Funding support United States, 1 items
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 ReportPDB-ID: 6vnw

SummaryFull reportAbout validation report
History
DepositionJan 29, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vnw
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21251.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 320 pix.
= 416. Å
1.3 Å/pix.
x 320 pix.
= 416. Å
1.3 Å/pix.
x 320 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.24943139 - 0.40319476
Average (Standard dev.)0.00000533185 (±0.0054252753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2490.4030.000

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Supplemental data

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Sample components

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Entire BBSome complex

EntireName: BBSome complex / Number of components: 9

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Component #1: protein, BBSome complex

ProteinName: BBSome complex / Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organ or tissue: retina

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Component #2: protein, Bardet-Biedl syndrome 18 protein

ProteinName: Bardet-Biedl syndrome 18 proteinBardet–Biedl syndrome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.070502 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #3: protein, Bardet-Biedl syndrome 2 protein homolog

ProteinName: Bardet-Biedl syndrome 2 protein homologBardet–Biedl syndrome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 79.911484 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #4: protein, Bardet-Biedl syndrome 4 protein homolog

ProteinName: Bardet-Biedl syndrome 4 protein homologBardet–Biedl syndrome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.289133 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #5: protein, Bardet-Biedl syndrome 5 protein homolog

ProteinName: Bardet-Biedl syndrome 5 protein homologBardet–Biedl syndrome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.880984 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #6: protein, Bardet-Biedl syndrome 7 protein homolog

ProteinName: Bardet-Biedl syndrome 7 protein homologBardet–Biedl syndrome
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.471375 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #7: protein, Tetratricopeptide repeat domain 8

ProteinName: Tetratricopeptide repeat domain 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.686406 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #8: protein, Bardet-Biedl syndrome 9

ProteinName: Bardet-Biedl syndrome 9Bardet–Biedl syndrome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 99.230914 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Component #9: protein, BBS1 domain-containing protein

ProteinName: BBS1 domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.939141 kDa
SourceSpecies: Bovine (cattle)
Source (natural)Organ or tissue: retina

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / 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
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 80 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 560777
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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