[English] 日本語
Yorodumi
- EMDB-10618: The human core BBSome complex (BBS 1,4,5,8,9,18) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10618
TitleThe human core BBSome complex (BBS 1,4,5,8,9,18)
Map data
Sample
  • Complex: Human BBSome core complex
    • Protein or peptide: Bardet-Biedl syndrome 5 protein
Keywordsciliary transport / Arl6 effector / adaptor protein / complex / PROTEIN TRANSPORT
Function / homology
Function and homology information


RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / BBSome / melanosome transport / motile cilium assembly / BBSome-mediated cargo-targeting to cilium / response to stimulus / phosphatidylinositol-3-phosphate binding / ciliary membrane / heart looping / axoneme ...RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / BBSome / melanosome transport / motile cilium assembly / BBSome-mediated cargo-targeting to cilium / response to stimulus / phosphatidylinositol-3-phosphate binding / ciliary membrane / heart looping / axoneme / centriolar satellite / cilium assembly / intracellular transport / visual perception / ciliary basal body / protein transport / cytosol
Similarity search - Function
Bardet-Biedl syndrome 5 protein / DM16 repeat / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / Bardet-Biedl syndrome 5 protein / Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc.
Similarity search - Domain/homology
Bardet-Biedl syndrome 5 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKlink BU / Raunser S
Funding support Germany, 1 items
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, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xtb
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xtb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10618.png

Downloads & links

-
Map

FileDownload / File: emd_10618.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0175 / Movie #1: 0.0175
Minimum - Maximum-0.033580124 - 0.06300068
Average (Standard dev.)0.00022122166 (±0.002166431)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0340.0630.000

-
Supplemental data

-
Sample components

-
Entire : Human BBSome core complex

EntireName: Human BBSome core complex
Components
  • Complex: Human BBSome core complex
    • Protein or peptide: Bardet-Biedl syndrome 5 protein

-
Supramolecule #1: Human BBSome core complex

SupramoleculeName: Human BBSome core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: BBSome core complex containing BBS1,4,5,8,9 and 18. Only BBS5 was modelled into this map since we obtained another map with higher resolution for the other subunits (see related entry)
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Bardet-Biedl syndrome 5 protein

MacromoleculeName: Bardet-Biedl syndrome 5 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.797926 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH SLALSRVNVS VGYNCILNIT TRTANSKLR GQTEALYILT KCNSTRFEFI FTNLVPGSPR LFTSVMAVHR AYETSKMYRD FKLRSALIQN KQLRLLPQEH V YDKINGVW ...String:
MSVLDALWED RDVRFDLSAQ QMKTRPGEVL IDCLDSIEDT KGNNGDRGRL LVTNLRILWH SLALSRVNVS VGYNCILNIT TRTANSKLR GQTEALYILT KCNSTRFEFI FTNLVPGSPR LFTSVMAVHR AYETSKMYRD FKLRSALIQN KQLRLLPQEH V YDKINGVW NLSSDQGNLG TFFITNVRIV WHANMNDSFN VSIPYLQIRS IKIRDSKFGL ALVIESSQQS GGYVLGFKID PV EKLQESV KEINSLHKVY SASPIFGVDY EMEEKPQPLE ALTVEQIQDD VEIDSDGHTD AFVAYFADGN KQQDREPVFS EEL GLAIEK LKDGFTLQGL WEVMS

UniProtKB: Bardet-Biedl syndrome 5 protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.08 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTRIS-HCL
150.0 mMNaCl
0.1 mMTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK III
Details: double blot with 2 minutes incubation after first sample application.
DetailsThe sample was cross linked with 0.5% glutaraldehyde

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number real images: 15266 / Average exposure time: 15.0 sec. / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2831329
Startup modelType of model: INSILICO MODEL
In silico model: An initial model for BBS5 was generated de novo using RaptorX.
Details: The model was changed to polyalanine
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.2-1.3) / Software - details: Meridien / Number images used: 180654
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.2-1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.2-1.3) / Software - details: Meridien
Final 3D classificationNumber classes: 4 / Software - Name: SPHIRE (ver. 1.2-1.3) / Software - details: Sort3D
Details: The subunit BBS5 was located in a subset of 180654 particles identified by 3D sorting.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more