[English] 日本語
Yorodumi
- PDB-6xt9: Subunits BBS 1,4,8,9,18 of the human BBSome complex -

+
Open data


ID or keywords:

Loading...

-
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 proteinBardet–Biedl syndrome
  • Bardet-Biedl syndrome 4 proteinBardet–Biedl syndrome
  • 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 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / receptor localization to non-motile cilium / BBSome / retinal rod cell development / negative regulation of appetite by leptin-mediated signaling pathway / photoreceptor cell outer segment organization / regulation of cilium beat frequency involved in ciliary motility / smoothened binding ...regulation of non-motile cilium assembly / protein localization to photoreceptor outer segment / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / receptor localization to non-motile cilium / BBSome / retinal rod cell development / negative regulation of appetite by leptin-mediated signaling pathway / photoreceptor cell outer segment organization / regulation of cilium beat frequency involved in ciliary motility / smoothened binding / ciliary transition zone / microtubule anchoring at centrosome / sensory processing / protein localization to organelle / photoreceptor connecting cilium / melanosome transport / patched binding / Golgi to plasma membrane protein transport / ventricular system development / BBSome-mediated cargo-targeting to cilium / negative regulation of actin filament polymerization / positive regulation of cilium assembly / striatum development / protein localization to cilium / maintenance of protein location in nucleus / positive regulation of multicellular organism growth / non-motile cilium assembly / non-motile cilium / negative regulation of systemic arterial blood pressure / brain morphogenesis / regulation of stress fiber assembly / photoreceptor cell maintenance / retina homeostasis / motile cilium / centrosome cycle / protein localization to centrosome / response to stimulus / negative regulation of GTPase activity / ciliary membrane / fat pad development / adult behavior / beta-tubulin binding / heart looping / pericentriolar material / dendrite development / fat cell differentiation / face development / spermatid development / axoneme / dynactin binding / social behavior / alpha-tubulin binding / mitotic cytokinesis / regulation of lipid metabolic process / intracellular transport / cilium assembly / centriolar satellite / photoreceptor outer segment / photoreceptor inner segment / visual perception / centriole / ciliary basal body / regulation of cytokinesis / neural tube closure / hippocampus development / neuron migration / cilium / cerebral cortex development / microtubule cytoskeleton organization / sensory perception of smell / protein-macromolecule adaptor activity / protein transport / negative regulation of gene expression / centrosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Bardet-Biedl syndrome 4 protein / Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / Cilia BBSome complex subunit 10 / Parathyroid hormone-responsive B1 / PTHB1, N-terminal domain / PTHB1, C-terminal domain / PTHB1 N-terminus / PTHB1 C-terminus / Bardet-Biedl syndrome 1 protein ...Bardet-Biedl syndrome 4 protein / Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / Cilia BBSome complex subunit 10 / Parathyroid hormone-responsive B1 / PTHB1, N-terminal domain / PTHB1, C-terminal domain / PTHB1 N-terminus / PTHB1 C-terminus / Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 1, N-terminal / Ciliary BBSome complex subunit 1 / Tetratricopeptide repeat / : / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Tetratricopeptide repeat domain 8 isoform 2 / BBSome-interacting protein 1 / Protein PTHB1 / Bardet-Biedl syndrome 1 protein / Bardet-Biedl syndrome 4 protein
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10617
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

#1: Protein Bardet-Biedl syndrome 1 protein / Bardet–Biedl syndrome / 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 / Bardet–Biedl syndrome


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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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-HCLTris1
2150 mMNaClSodium chloride1
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

-
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 FIELDBright-field microscopy / 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

-
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

+
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://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