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- EMDB-10617: Subunits BBS 1,4,8,9,18 of the human BBSome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10617
TitleSubunits BBS 1,4,8,9,18 of the human BBSome complex
Map data
Sample
  • Complex: BBSome core complex
    • Protein or peptide: Bardet-Biedl syndrome 1 protein
    • Protein or peptide: Bardet-Biedl syndrome 4 protein
    • Protein or peptide: Tetratricopeptide repeat domain 8 isoform 2
    • Protein or peptide: Protein PTHB1
    • Protein or peptide: BBSome-interacting protein 1
Keywordsciliary transport / Arl6 effector / adaptor protein / complex / PROTEIN TRANSPORT
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 / microtubule anchoring at centrosome / 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 / microtubule anchoring at centrosome / smoothened binding / regulation of cilium beat frequency involved in ciliary motility / sensory processing / protein localization to organelle / ciliary transition zone / melanosome transport / photoreceptor connecting cilium / patched binding / ventricular system development / negative regulation of actin filament polymerization / BBSome-mediated cargo-targeting to cilium / striatum development / Golgi to plasma membrane protein transport / positive regulation of cilium assembly / positive regulation of multicellular organism growth / response to stimulus / non-motile cilium assembly / maintenance of protein location in nucleus / photoreceptor cell maintenance / protein localization to cilium / regulation of stress fiber assembly / brain morphogenesis / non-motile cilium / negative regulation of systemic arterial blood pressure / retina homeostasis / motile cilium / centrosome cycle / protein localization to centrosome / negative regulation of GTPase activity / ciliary membrane / fat pad development / adult behavior / pericentriolar material / beta-tubulin binding / heart looping / fat cell differentiation / dendrite development / face development / axoneme / dynactin binding / social behavior / regulation of lipid metabolic process / centriolar satellite / spermatid development / mitotic cytokinesis / photoreceptor outer segment / alpha-tubulin binding / cilium assembly / intracellular transport / visual perception / centriole / photoreceptor inner segment / ciliary basal body / regulation of cytokinesis / neural tube closure / hippocampus development / neuron migration / cerebral cortex development / cilium / microtubule cytoskeleton organization / sensory perception of smell / protein transport / protein-macromolecule adaptor activity / negative regulation of gene expression / centrosome / membrane / nucleus / cytoplasm / cytosol
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 / : / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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) releaseJan 29, 2020-
Map releaseJan 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-6xt9
  • Surface level: 0.015
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10617.png

Downloads & links

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Map

FileDownload / File: emd_10617.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: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.060557723 - 0.11145467
Average (Standard dev.)0.00021456317 (±0.002398998)
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-0.0610.1110.000

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Supplemental data

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Mask #1

Fileemd_10617_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10617_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_10617_half_map_2.map
Projections & Slices
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Sample components

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Entire : BBSome core complex

EntireName: BBSome core complex
Components
  • Complex: BBSome core complex
    • Protein or peptide: Bardet-Biedl syndrome 1 protein
    • Protein or peptide: Bardet-Biedl syndrome 4 protein
    • Protein or peptide: Tetratricopeptide repeat domain 8 isoform 2
    • Protein or peptide: Protein PTHB1
    • Protein or peptide: BBSome-interacting protein 1

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Supramolecule #1: BBSome core complex

SupramoleculeName: BBSome core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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)
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Bardet-Biedl syndrome 1 protein

MacromoleculeName: Bardet-Biedl syndrome 1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.159266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAASSSDSD ACGAESNEAN SKWLDAHYDP MANIHTFSAC LALADLHGDG EYKLVVGDLG PGGQQPRLKV LKGPLVMTES PLPALPAAA ATFLMEQHEP RTPALALASG PCVYVYKNLR PYFKFSLPQL PPNPLEQDLW NQAKEDRIDP LTLKEMLESI R ETAEEPLS ...String:
MAAASSSDSD ACGAESNEAN SKWLDAHYDP MANIHTFSAC LALADLHGDG EYKLVVGDLG PGGQQPRLKV LKGPLVMTES PLPALPAAA ATFLMEQHEP RTPALALASG PCVYVYKNLR PYFKFSLPQL PPNPLEQDLW NQAKEDRIDP LTLKEMLESI R ETAEEPLS IQSLRFLQLE LSEMEAFVNQ HKSNSIKRQT VITTMTTLKK NLADEDAVSC LVLGTENKEL LVLDPEAFTI LA KMSLPSV PVFLEVSGQF DVEFRLAAAC RNGNIYILRR DSKHPKYCIE LSAQPVGLIR VHKVLVVGST QDSLHGFTHK GKK LWTVQM PAAILTMNLL EQHSRGLQAV MAGLANGEVR IYRDKALLNV IHTPDAVTSL CFGRYGREDN TLIMTTRGGG LIIK ILKRT AVFVEGGSEV GPPPAQAMKL NVPRKTRLYV DQTLREREAG TAMHRAFQTD LYLLRLRAAR AYLQALESSL SPLST TARE PLKLHAVVQG LGPTFKLTLH LQNTSTTRPV LGLLVCFLYN EALYSLPRAF FKVPLLVPGL NYPLETFVES LSNKGI SDI IKVLVLREGQ SAPLLSAHVN MPGSEGLAAA

UniProtKB: Bardet-Biedl syndrome 1 protein

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Macromolecule #2: Bardet-Biedl syndrome 4 protein

MacromoleculeName: Bardet-Biedl syndrome 4 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.46302 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGPM AEERVATRTQ FPVSTESQKP RQKKAPEFPI LEKQNWLIHL HYIRKDYEAC KAVIKEQLQE TQGLCEYAIY VQALIFRLE GNIQESLELF QTCAVLSPQS ADNLKQVARS LFLLGKHKAA IEVYNEAAKL NQKDWEISHN LGVCYIYLKQ F NKAQDQLH ...String:
MHHHHHHGPM AEERVATRTQ FPVSTESQKP RQKKAPEFPI LEKQNWLIHL HYIRKDYEAC KAVIKEQLQE TQGLCEYAIY VQALIFRLE GNIQESLELF QTCAVLSPQS ADNLKQVARS LFLLGKHKAA IEVYNEAAKL NQKDWEISHN LGVCYIYLKQ F NKAQDQLH NALNLNRHDL TYIMLGKIHL LEGDLDKAIE VYKKAVEFSP ENTELLTTLG LLYLQLGIYQ KAFEHLGNAL TY DPTNYKA ILAAGSMMQT HGDFDVALTK YRVVACAVPE SPPLWNNIGM CFFGKKKYVA AISCLKRANY LAPFDWKILY NLG LVHLTM QQYASAFHFL SAAINFQPKM GELYMLLAVA LTNLEDIENA KRAYAEAVHL DKCNPLVNLN YAVLLYNQGE KKNA LAQYQ EMEKKVSLLK DNSSLEFDSE MVEMAQKLGA ALQVGEALVW TKPVKDPKSK HQTTSTSKPA SFQQPLGSNQ ALGQA MSSA AAYRTLPSGA GGTSQFTKPP SLPLEPEPAV ESSPTETSEQ IREK

UniProtKB: Bardet-Biedl syndrome 4 protein

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Macromolecule #3: Tetratricopeptide repeat domain 8 isoform 2

MacromoleculeName: Tetratricopeptide repeat domain 8 isoform 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.702539 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDDDDKA GPMSSEMEPL LLAWSYFRRR KFQLCADLCT QMLEKSPYDQ AAWILKARAL TEMVYIDEID VDQEGIAEMM LDENAIAQV PRPGTSLKLP GTNQTGGPSQ AVRPITQAGR PITGFLRPST QSGRPGTMEQ AIRTPRTAYT ARPITSSSGR F VRLGTASM ...String:
MDYKDDDDKA GPMSSEMEPL LLAWSYFRRR KFQLCADLCT QMLEKSPYDQ AAWILKARAL TEMVYIDEID VDQEGIAEMM LDENAIAQV PRPGTSLKLP GTNQTGGPSQ AVRPITQAGR PITGFLRPST QSGRPGTMEQ AIRTPRTAYT ARPITSSSGR F VRLGTASM LTSPDGPFIN LSRLNLTKYS QKPKLAKALF EYIFHHENDV KTALDLAALS TEHSQYKDWW WKVQIGKCYY RL GMYREAE KQFKSALKQQ EMVDTFLYLA KVYVSLDQPV TALNLFKQGL DKFPGEVTLL CGIARIYEEM NNMSSAAEYY KEV LKQDNT HVEAIACIGS NHFYSDQPEI ALRFYRRLLQ MGIYNGQLFN NLGLCCFYAQ QYDMTLTSFE RALSLAENEE EAAD VWYNL GHVAVGIGDT NLAHQCFRLA LVNNNNHAEA YNNLAVLEMR KGHVEQARAL LQTASSLAPH MYEPHFNFAT ISDKI GDLQ RSYVAAQKSE AAFPDHVDTQ HLIKQLRQHF AML

UniProtKB: Tetratricopeptide repeat domain 8 isoform 2

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Macromolecule #4: Protein PTHB1

MacromoleculeName: Protein PTHB1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.383914 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSLFKARDWW STILGDKEEF DQGCLCLANV DNSGNGQDKI IVGSFMGYLR IFSPHPAKTG DGAQAEDLLL EVDLRDPVLQ VEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN QCQMKLMYEH NLQRTACNMT YGSFGGVKGR DLICIQSMDG M LMVFEQES ...String:
MSLFKARDWW STILGDKEEF DQGCLCLANV DNSGNGQDKI IVGSFMGYLR IFSPHPAKTG DGAQAEDLLL EVDLRDPVLQ VEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN QCQMKLMYEH NLQRTACNMT YGSFGGVKGR DLICIQSMDG M LMVFEQES YAFGRFLPGF LLPGPLAYSS RTDSFLTVSS CQQVESYKYQ VLAFATDADK RQETEQQKLG SGKRLVVDWT LN IGEQALD ICIVSFNQSA SSVFVLGERN FFCLKDNGQI RFMKKLDWSP SCFLPYCSVS EGTINTLIGN HNNMLHIYQD VTL KWATQL PHIPVAVRVG CLHDLKGVIV TLSDDGHLQC SYLGTDPSLF QAPNVQSREL NYDELDVEMK ELQKIIKDVN KSQG VWPMT EREDDLNVSV VVSPNFDSVS QATDVEVGTD LVPSVTVKVT LQNRVILQKA KLSVYVQPPL ELTCDQFTFE FMTPD LTRT VSFSVYLKRS YTPSELEGNA VVSYSRPTDR NPDGIPRVIQ CKFRLPLKLI CLPGQPSKTA SHKITIDTNK SPVSLL SLF PGFASQSDDD QVNVMGFHFL GGARITVLAS KTSQRYRIQS EQFEDLWLIT NELILRLQEY FEKQGVKDFA CSFSGSI PL QEYFELIDHH FELRINGEKL EELLSERAVQ FRAIQRRLLA RFKDKTPAPL QHLDTLLDGT YKQVIALADA VEENQGNL F QSFTRLKSAT HLVILLIALW QKLSADQVAI LEAAFLPLQE DTQELGWEET VDAAISHLLK TCLSKSSKEQ ALNLNSQLN IPKDTSQLKK HITLLCDRLS KGGRLCLSTD AAAPQTMVMP GGCTTIPESD LEERSVEQDS TELFTNHRHL TAETPRPEVS PLQGVSE

UniProtKB: Protein PTHB1

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Macromolecule #5: BBSome-interacting protein 1

MacromoleculeName: BBSome-interacting protein 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.430824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KGAGLEVLFQ GPKRAEFMLK AAAKRPELSG KNTISNNSDM AEVKSMFREV LPKQGPLFV EDIMTMVLCK PKLLPLKSLT LEKLEKMHQA AQNTIRQQEM AEKDQRQITH

UniProtKB: BBSome-interacting protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.08 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMTRIS-HCL
150.0 mMNaCl
0.1 mMTCEP
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
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

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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

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Image processing

Particle selectionNumber selected: 2831329
Startup modelType of model: INSILICO MODEL
In silico model: Initial models were generated de novo using RaptorX for most of the structure.
Details: For building an atomic model of the beta propeller domains, we used the two available crystal structures of the beta propeller domains of C. reinhardtii BBS1 (PDB ID 4V0M) and of human BBS9 ...Details: For building an atomic model of the beta propeller domains, we used the two available crystal structures of the beta propeller domains of C. reinhardtii BBS1 (PDB ID 4V0M) and of human BBS9 (PDB ID 4YD8) as starting points.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.2-1.3) / Software - details: Meridien / Number images used: 862114
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

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