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- EMDB-7839: BBSome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-7839
TitleBBSome complex
Map dataprimary map
Sample
  • Complex: BBSome
    • Protein or peptide: BBS5
    • Protein or peptide: BBS9
    • Protein or peptide: BBS1
    • Protein or peptide: BBS7
    • Protein or peptide: BBS8
    • Protein or peptide: BBS18
    • Protein or peptide: BBS4
    • Protein or peptide: BBS2
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsChou H / Apelt L / Farrell DP / White SR / Woodsmith J / Svetlov V / Goldstein JS / Nager AR / Li Z / Muller J ...Chou H / Apelt L / Farrell DP / White SR / Woodsmith J / Svetlov V / Goldstein JS / Nager AR / Li Z / Muller J / Dollfus H / Nudler E / Stelzl U / DiMaio F / Walz T / Nachury NV
CitationJournal: Structure / Year: 2019
Title: The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach.
Authors: Hui-Ting Chou / Luise Apelt / Daniel P Farrell / Susan Roehl White / Jonathan Woodsmith / Vladimir Svetlov / Jaclyn S Goldstein / Andrew R Nager / Zixuan Li / Jean Muller / Hélène Dollfus ...Authors: Hui-Ting Chou / Luise Apelt / Daniel P Farrell / Susan Roehl White / Jonathan Woodsmith / Vladimir Svetlov / Jaclyn S Goldstein / Andrew R Nager / Zixuan Li / Jean Muller / Hélène Dollfus / Evgeny Nudler / Ulrich Stelzl / Frank DiMaio / Maxence V Nachury / Thomas Walz /
Abstract: The unique membrane composition of cilia is maintained by a diffusion barrier at the transition zone that is breached when the BBSome escorts signaling receptors out of cilia. Understanding how the ...The unique membrane composition of cilia is maintained by a diffusion barrier at the transition zone that is breached when the BBSome escorts signaling receptors out of cilia. Understanding how the BBSome removes proteins from cilia has been hampered by a lack of structural information. Here, we present a nearly complete Cα model of BBSome purified from cow retina. The model is based on a single-particle cryo-electron microscopy density map at 4.9-Å resolution that was interpreted with the help of comprehensive Rosetta-based structural modeling constrained by crosslinking mass spectrometry data. We find that BBSome subunits have a very high degree of interconnectivity, explaining the obligate nature of the complex. Furthermore, like other coat adaptors, the BBSome exists in an autoinhibited state in solution and must thus undergo a conformational change upon recruitment to membranes by the small GTPase ARL6/BBS3. Our model provides the first detailed view of the machinery enabling ciliary exit.
History
DepositionMay 1, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseAug 21, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7839.png

Downloads & links

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Map

FileDownload / File: emd_7839.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å		1.23 Å/pix.
x 320 pix.
= 393.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.037584525 - 0.11622269
Average (Standard dev.)0.0002530068 (±0.003536107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 393.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0380.1160.000

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Supplemental data

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Sample components

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Entire : BBSome

EntireName: BBSome
Components
  • Complex: BBSome
    • Protein or peptide: BBS5
    • Protein or peptide: BBS9
    • Protein or peptide: BBS1
    • Protein or peptide: BBS7
    • Protein or peptide: BBS8
    • Protein or peptide: BBS18
    • Protein or peptide: BBS4
    • Protein or peptide: BBS2

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Supramolecule #1: BBSome

SupramoleculeName: BBSome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: BBS5

MacromoleculeName: BBS5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MSVLDALWED RDVRFDVSSQ QMKTRPGEVL IDCLDSVEDT KGNNGDRGRL LVTNLRIVWH SLALPRVNL SIGYNCILNI TTRTANSKLR GQTEALYVLT KCNSTRFEFI FTNLVPGSPR L YTSLIAVH RAYETSKMYR DFKLRSALIQ NKQLRLLPQE NVYNKINGVW ...String:
MSVLDALWED RDVRFDVSSQ QMKTRPGEVL IDCLDSVEDT KGNNGDRGRL LVTNLRIVWH SLALPRVNL SIGYNCILNI TTRTANSKLR GQTEALYVLT KCNSTRFEFI FTNLVPGSPR L YTSLIAVH RAYETSKMYR DFKLRSALIQ NKQLRLLPQE NVYNKINGVW NLSSDQGNLG TF FITNVRI VWHANMNDSF NVSIPYLQIR SVKIRDSKFG LALVIESSQQ SGGYVLGFKI DPV EKLQES VKEINSLHKV YSANPIFGVD YEMEEKPQPL EALTVKQIQD DVEIDSDDHT DAFV AYFAD GNKQQDREPV FSEELGLAIE KLKDGFTLQG LWEVMN

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Macromolecule #2: BBS9

MacromoleculeName: BBS9 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MSLFKARDWW STVLGDKEEF DQGCLCLADV DNTGNGQDKI IVGSFMGYLR IFNPHPVKTG DGAQAEDLL LEVHLRDPIL QVEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN Q YQIKLMYE HNLQRTACNM TYGSFGGVKG RDLICIQSVD GMLMVFEQES ...String:
MSLFKARDWW STVLGDKEEF DQGCLCLADV DNTGNGQDKI IVGSFMGYLR IFNPHPVKTG DGAQAEDLL LEVHLRDPIL QVEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN Q YQIKLMYE HNLQRTACNM TYGSFGGVKG RDLICIQSVD GMLMVFEQES YAFGRFLPGS LL PGPLAYS SRTDSFITVS SCHQVESYKY QVLAFATDAD KRQETEQQKH GSGKRLVVDW TLN IGEQAI DICIVSFIQS ASSVFVLGER NFFCLKDNGQ IQFMKKLDYS PSCFLPYCSV SEGT INTLI GNHNNMLHIY QDVTLKWATQ LPHVPVAVRV GCLHDLKGVI VTLSDDGHLQ CSYLG TDPS LFQAPKVESR ELNYDELDME LKELQKVIKN VNKSQDVWPL TEREDDLKVS AMVSPN FDS VSQATDVEVG ADLVPSVTVK VTLKNRVALQ KIKLSIYVQP PLVLTGDQFT FEFMAPE MT RTVGFSVYLK GSYSPPELEG NAVVSYSRPT ERNPDGIPRV SQCKFRLPLK LVCLPGQP S KTASHKLTID TNKSPVSLLS LFPGFAKQSE DDQVNVMGFR FLGGSQVTLL ASKTSQRYR IQSEQFEDLW LITNELIIRL QEYFEKQGIK DFTCSFSGSV PLEEYFELID HHFELRINGE KLEELLSER AVQFRAIQRR LLTRFKDKTP APLQHLDTLL DGTYKQVIAL ADAVEENQDN L FQSFTRLK SATHLVILLI GLWQKLSADQ IAILEAAFLP LQQDTQELGW EETVDAALSH LL KTCLSKS SKEQALNLNS QLGIPKDTSQ LKKHITLFCD RLAKGGRLCL STDAAAPQTM VMP GGCATI PESDLEGRSI DQDSSELFTN HKHLMVETPV PEVSPLQGVT E

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Macromolecule #3: BBS1

MacromoleculeName: BBS1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MAATSSSDSD GGKGESSEAN SKWLDSLSDS MANIHTFSAC LALADFHGDG EYKLAMGDLG PDGRQPRLK VLKGHTLVSQ KPLPDLPAAA VTFLMASHEP RTPALAIASG PCVYVYKNLK P YFKFSLPS LPTNPLEQDL WNQAKEDQID PLTLKEMLEG IREKAEVPLS ...String:
MAATSSSDSD GGKGESSEAN SKWLDSLSDS MANIHTFSAC LALADFHGDG EYKLAMGDLG PDGRQPRLK VLKGHTLVSQ KPLPDLPAAA VTFLMASHEP RTPALAIASG PCVYVYKNLK P YFKFSLPS LPTNPLEQDL WNQAKEDQID PLTLKEMLEG IREKAEVPLS VQSLRFLPLE LS EMEAFVN QHKSKSIRRQ TVITTMTTLK KNLADEDAVS CLVLGTENKE LLVLDPEAFT ILA KMSLPS VPAFLEASGQ FDVEFRLAAA CRNGSIYILR RDSKRPKYCI ELGAQPVGLV GVHK VLVVG SNQDSLHGFT YKGKRLWTVQ MPAAILAMNL LEQHSRGLQA VMAALANEEV RIYHD KVLL NVIRTPEAVT SLCFGRYGRE DNTLIMTTLG GGLIIKILKR TAVFAEGGGE AGPPPS QAI KLNVPRKTRL YVDQTLRERE AGTAMHRTFQ ADLYLLRLRA ARAYVQALES SLSPVSL TA REPLKLHAVV QGLGPTFKLT LHLQNTSTAR PILGLVVCFL YNEVLYALPR AFFKVPLL V PGLNYPLETF VKSLSDKGIS DIIKVLVLRE GQSTPLLSAH INMPMSEGLA AD

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Macromolecule #4: BBS7

MacromoleculeName: BBS7 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MLFSSSVPFV GVTSQKTMKL LPASKHRATQ KVVVGDHDGI VMCFGMKKGE AVTVFKTLPG QKIARLELG GALNTPQEKI FIAAGSEIRG FTKRGKQFLS FETNLTESIK AMHISGSDLF L SASYIYNH YCDCKDQHYY LSGDKINDVI CLPVERLLRE VPVLACQDRV ...String:
MLFSSSVPFV GVTSQKTMKL LPASKHRATQ KVVVGDHDGI VMCFGMKKGE AVTVFKTLPG QKIARLELG GALNTPQEKI FIAAGSEIRG FTKRGKQFLS FETNLTESIK AMHISGSDLF L SASYIYNH YCDCKDQHYY LSGDKINDVI CLPVERLLRE VPVLACQDRV LRVLQGSDVT YE IEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLGLIQ ITTSKPIHKW EIRNEKKRGG ILC VDSFDI VGDGVKDLLV GRDDGMVEVY GFDNANEPVL RFDHTLSESV TSIQGGCVGK DGYD EIVVS TYSGWITGLT TEPVHKESGP GEELKFNQEM QNKISSLRSE LEQLQYKVLQ EREKY QQSS QSSKAKSAVP SFSVNDKFTL NKDDASYSLI LEVQTAIDNV LIQSDVPIDL LDVDKN SAV VSFSSCDSES NDNFLLATYR CQANTTRLEL KIRSIEGQYG TLQAYVTPRI QPKTCQV RQ YHIKPLSLHQ RTHFIDHDRP MNTLTLTGQF SFSELHSWVV FCMPEVPEKP PAGECVTF Y FQNTFLDTQL ESTYRKGEGV FKSDNISTIS ILKDVLSKEA TKRKINLNIS YEINEVSVK HTLKLIHPKL EYQLLLAKKV QLIDALKELQ VHEGNTNFLI PEYRCILEEA DHLQEEYKKQ PAHLERLYG MITDLFIDKF KFKGTNVKTK VPLLLEILDS YDQNALIAFF DAA

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Macromolecule #5: BBS8

MacromoleculeName: BBS8 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: APASDMEPLL LAWSYFRRRR FQLCADLCTQ MLEKSPCDQA AWILKARALT EMVYVDEIDV DEEGIAEMI LDENAIAQVP RPGTSLKLPG TNQTGGPSPA VRPVTQAGRP ITGFLRPSTQ S GRPGTIEQ AIKTPRTAYT ARPIASSSGR FVRLGTASML TSPDGPFINL ...String:
APASDMEPLL LAWSYFRRRR FQLCADLCTQ MLEKSPCDQA AWILKARALT EMVYVDEIDV DEEGIAEMI LDENAIAQVP RPGTSLKLPG TNQTGGPSPA VRPVTQAGRP ITGFLRPSTQ S GRPGTIEQ AIKTPRTAYT ARPIASSSGR FVRLGTASML TSPDGPFINL SRLNLAKYAQ KP KLAKALF EYIFHHENDV KTALDLAALS TEHSQYKDWW WKVQIGKCYY RLGLYREAEK QFK SALKQQ EMVDTFLYLA KVYISLDQPL TALNLFKQGL DKFPGEVTLL CGIARIYEEM NNIS SATEY YKEVLKQDNT HVEAIACIGS NHFYTDQPEV ALRFYRRLLQ MGVYNCQLFN NLGLC CFYA QQYDMTLTSF ERALSLAENE EEVADVWYNL GHVAVGTGDT NLAHQCFRLA LVSNNQ HAE AYNNLAVLEM RRGHVEQAKA LLQTASSLAP HMYEPHFNFA TISDKIGDLQ RSYAAAK KS EAAFPDHVDT QHLIKQLEQH FAML

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Macromolecule #6: BBS18

MacromoleculeName: BBS18 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString:
MLSAAHKSFC FPSATQDETV SNISDMAETK SMFREVLPKQ DLGQLYVEDI TTMVLCKPKL LPLKSLTLE KLEKMQQAAQ DTIHQQEMTE KEQKITH

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Macromolecule #7: BBS4

MacromoleculeName: BBS4 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MAEEKLSART QLPVSAESQK PVLKKAPEFP ILEKQNWLIH LYYIQKDYEA CKAVIKEQLQ ETHGLCEYA IYVQALIFRL EGNIQESLRL FQMCAFLSPQ CADNLKQVAR SLFLLGKHKA A IEVYNEAA KLNQKDWEIC HNLGVCYIYL KQFDKAQDQL HNALHLNRHD ...String:
MAEEKLSART QLPVSAESQK PVLKKAPEFP ILEKQNWLIH LYYIQKDYEA CKAVIKEQLQ ETHGLCEYA IYVQALIFRL EGNIQESLRL FQMCAFLSPQ CADNLKQVAR SLFLLGKHKA A IEVYNEAA KLNQKDWEIC HNLGVCYIYL KQFDKAQDQL HNALHLNRHD LTYIMLGKIF LL KGDLDKA IEIYKKAVEF SPENTELLTT LGLLYLQLGI YQKAFEHLGN TLTYDPTNYK AIL AAGSMM QTHGDFDVAL TKYKVVACAV IESPPLWNNI GMCFFGKKKY VAAISCLKRA NYLA PLDWK ILYNLGLVHL TMQQYASAFH FLSAAINFQP KMGELYMLLA VALTNLEDSE NAKRA YEEA VRLDKCNPLV NLNYAVLLYN QGEKRDALAQ YQEMEKKVNL LKYSSSLEFD PEMVEV AQK LGAALQVGEA LVWTKPVKDP KSKHQTASTS KAAGFQQPLG SNQALGQAMS SAATCRK LS SGAGGTSQLT KPPSLPLEPE PTVEAQPTEA SAQTREK

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Macromolecule #8: BBS2

MacromoleculeName: BBS2 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MLQPVFTLKL RHKISPRMVA VGRYDGTHPC LAAATQAGKV FIHNPHSRSQ HLGAPRVLQS PLESDVSLL NINQTVSCLT AGVLNPELGY DALLVGTQTN LLAYDVYNNS DLFYREVADG A SAIVLGTL GDITSPLAII GGNCALQGFN HEGNDLFWTV TGDNVHSLAL ...String:
MLQPVFTLKL RHKISPRMVA VGRYDGTHPC LAAATQAGKV FIHNPHSRSQ HLGAPRVLQS PLESDVSLL NINQTVSCLT AGVLNPELGY DALLVGTQTN LLAYDVYNNS DLFYREVADG A SAIVLGTL GDITSPLAII GGNCALQGFN HEGNDLFWTV TGDNVHSLAL CDFDGDGKKE LL VGSEDFD IRVFKEDEIV AEMSETEIIT SLCPMYGSRF GYALSNGTVG VYDKTARYWR IKS KNQAMS IHAFDLNSDG VCELITGWSN GKVDARSDRT GEVIFKDNFS SAIAGVVEGD YRME GCQQL ICCSVDGEIR GYLPGTAEMR GNLMDISVEQ DLIRELSQKK QNLLLELRNY EENAK AELS SPLNEADGHR GVIPANTKHH TALSVSLGSE AQAAHAELCI STSNDTIIRA VLIFAE GVF AGESHVVHPS VHHLSSSVRI PITPPKDIPV DLHLKTFVGY RSSTQFHVFE LTRQLPR FS MYALTSPDPA SEPLSYVNFI IAERAQRVVM WLNQNFLLPE DTNIQNAPFQ VCFTSLRN G GQLYIKIKLS GEITVNTDDI DLAGDIIQSM ASFFAIEDLQ VEADFPVYFE ELRKVLVKV DEYHSVHQKL SADMADNSNL IRSLLVQAED ARLMRDMKTM KNRYKELYDL NKDLLNGYKI RCNNHTELL GSLKAVNQAI QRAGHLRVGK PKNQVITACR DAIRSNNINM LFRIMRVGTA S S

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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

BufferpH: 7 / Details: 40 mM HEPES, 220 mM NaCl, 1 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Average electron dose: 46.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Detector mode: SUPER-RESOLUTION / #1 - Average electron dose: 89.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 179280
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final 3D classificationSoftware - Name: RELION (ver. 1.3)
FSC plot (resolution estimation)

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