[English] 日本語
Yorodumi
- EMDB-21251: Cryo-EM structure of apo-BBSome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21251
TitleCryo-EM structure of apo-BBSome
Map data
Sample
  • Complex: BBSome complex
    • Protein or peptide: Bardet-Biedl syndrome 18 proteinBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 2 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 4 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 5 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 7 protein homologBardet–Biedl syndrome
    • Protein or peptide: Tetratricopeptide repeat domain 8Tetratricopeptide repeat
    • Protein or peptide: Bardet-Biedl syndrome 9Bardet–Biedl syndrome
    • Protein or peptide: BBS1 domain-containing protein
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


establishment of anatomical structure orientation / BBSome-mediated cargo-targeting to cilium / multi-ciliated epithelial cell differentiation / receptor localization to non-motile cilium / renal tubule development / BBSome / camera-type eye photoreceptor cell differentiation / smoothened binding / establishment of planar polarity / photoreceptor connecting cilium ...establishment of anatomical structure orientation / BBSome-mediated cargo-targeting to cilium / multi-ciliated epithelial cell differentiation / receptor localization to non-motile cilium / renal tubule development / BBSome / camera-type eye photoreceptor cell differentiation / smoothened binding / establishment of planar polarity / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / patched binding / olfactory bulb development / protein localization to cilium / non-motile cilium assembly / phosphatidylinositol-3-phosphate binding / establishment of epithelial cell apical/basal polarity / non-motile cilium / regulation of stress fiber assembly / motile cilium / centrosome cycle / ciliary membrane / pericentriolar material / fat cell differentiation / axoneme / intracellular transport / cilium assembly / centriolar satellite / ciliary basal body / axon guidance / protein localization to plasma membrane / multicellular organism growth / protein localization / cilium / regulation of protein localization / sensory perception of smell / protein-macromolecule adaptor activity / protein transport / RNA polymerase II-specific DNA-binding transcription factor binding / neuron projection / centrosome / membrane / cytoplasm
Similarity search - Function
Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 2 protein / Ciliary BBSome complex subunit 2, C-terminal domain / Ciliary BBSome complex subunit 2, middle region / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, C-terminal / Ciliary BBSome complex subunit 2, middle region / Bardet-Biedl syndrome 5 protein / DM16 repeat ...Bardet-Biedl syndrome 7 protein / Bardet-Biedl syndrome 2 protein / Ciliary BBSome complex subunit 2, C-terminal domain / Ciliary BBSome complex subunit 2, middle region / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, N-terminal / Ciliary BBSome complex subunit 2, C-terminal / Ciliary BBSome complex subunit 2, middle region / Bardet-Biedl syndrome 5 protein / DM16 repeat / Cilia BBSome complex subunit 10 / Tetratricopeptide repeat protein 8 / Bardet-Biedl syndrome 5 protein/sex-determination protein fem-3 / Bardet-Biedl syndrome 5 protein / Cilia BBSome complex subunit 10 / Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc. / 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 / TPR repeat / Tetratricopeptide 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 / PH-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Bardet-Biedl syndrome 5 protein homolog / Bardet-Biedl syndrome 9 / Bardet-Biedl syndrome 1 / Bardet-Biedl syndrome 7 protein homolog / Tetratricopeptide repeat domain 8 / BBSome interacting protein 1 / Bardet-Biedl syndrome 4 protein homolog / Bardet-Biedl syndrome 2 protein homolog
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYang S / Walz T
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.
History
DepositionJan 29, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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

emd_21251.png

Downloads & links

-
Map

FileDownload / File: emd_21251.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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.)0.0000053318463 (±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

-
Supplemental data

-
Sample components

-
Entire : BBSome complex

EntireName: BBSome complex
Components
  • Complex: BBSome complex
    • Protein or peptide: Bardet-Biedl syndrome 18 proteinBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 2 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 4 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 5 protein homologBardet–Biedl syndrome
    • Protein or peptide: Bardet-Biedl syndrome 7 protein homologBardet–Biedl syndrome
    • Protein or peptide: Tetratricopeptide repeat domain 8Tetratricopeptide repeat
    • Protein or peptide: Bardet-Biedl syndrome 9Bardet–Biedl syndrome
    • Protein or peptide: BBS1 domain-containing protein

-
Supramolecule #1: BBSome complex

SupramoleculeName: BBSome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 500 KDa

-
Macromolecule #1: Bardet-Biedl syndrome 18 protein

MacromoleculeName: Bardet-Biedl syndrome 18 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 8.070502 KDa
SequenceString:
MAETKSMFRE VLPKQGQLYV EDITTMVLCK PKLLPLKSLT LEKLEKMQQA AQDTIHQQEM TEKEQKITH

UniProtKB: BBSome interacting protein 1

-
Macromolecule #2: Bardet-Biedl syndrome 2 protein homolog

MacromoleculeName: Bardet-Biedl syndrome 2 protein homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 79.911484 KDa
SequenceString: MLQPVFTLKL RHKISPRMVA VGRYDGTHPC LAAATQAGKV FIHNPHSRSQ HLGAPRVLQS PLESDVSLLN INQTVSCLTA GVLNPELGY DALLVGTQTN LLAYDVYNNS DLFYREVADG ASAIVLGTLG DITSPLAIIG GNCALQGFNH EGNDLFWTVT G DNVHSLAL ...String:
MLQPVFTLKL RHKISPRMVA VGRYDGTHPC LAAATQAGKV FIHNPHSRSQ HLGAPRVLQS PLESDVSLLN INQTVSCLTA GVLNPELGY DALLVGTQTN LLAYDVYNNS DLFYREVADG ASAIVLGTLG DITSPLAIIG GNCALQGFNH EGNDLFWTVT G DNVHSLAL CDFDGDGKKE LLVGSEDFDI RVFKEDEIVA EMSETEIITS LCPMYGSRFG YALSNGTVGV YDKTARYWRI KS KNQAMSI HAFDLNSDGV CELITGWSNG KVDARSDRTG EVIFKDNFSS AIAGVVEGDY RMEGCQQLIC CSVDGEIRGY LPG TAEMRG NLMDISVEQD LIRELSQKKQ NLLLELRNYE ENAKAELSSP LNEADGHRGV IPANTKHHTA LSVSLGSEAQ AAHA ELCIS TSNDTIIRAV LIFAEGVFAG ESHVVHPSVH HLSSSVRIPI TPPKDIPVDL HLKTFVGYRS STQFHVFELT RQLPR FSMY ALTSPDPASE PLSYVNFIIA ERAQRVVMWL NQNFLLPEDT NIQNAPFQVC FTSLRNGGQL YIKIKLSGEI TVNTDD IDL AGDIIQSMAS FFAIEDLQVE ADFPVYFEEL RKVLVKVDEY HSVHQKLSAD MADNSNLIRS LLVQAEDARL MRDMKTM KN RYKELYDLNK DLLNGYKIRC NNHTELLGSL KAVNQAIQRA GHLRVGKPKN QVITACRDAI RSNNINMLFR IMRVGTAS S

UniProtKB: Bardet-Biedl syndrome 2 protein homolog

-
Macromolecule #3: Bardet-Biedl syndrome 4 protein homolog

MacromoleculeName: Bardet-Biedl syndrome 4 protein homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 58.289133 KDa
SequenceString: MAEEKLSART QLPVSAESQK PVLKKAPEFP ILEKQNWLIH LYYIQKDYEA CKAVIKEQLQ ETHGLCEYAI YVQALIFRLE GNIQESLRL FQMCAFLSPQ CADNLKQVAR SLFLLGKHKA AIEVYNEAAK LNQKDWEICH NLGVCYIYLK QFDKAQDQLH N ALHLNRHD ...String:
MAEEKLSART QLPVSAESQK PVLKKAPEFP ILEKQNWLIH LYYIQKDYEA CKAVIKEQLQ ETHGLCEYAI YVQALIFRLE GNIQESLRL FQMCAFLSPQ CADNLKQVAR SLFLLGKHKA AIEVYNEAAK LNQKDWEICH NLGVCYIYLK QFDKAQDQLH N ALHLNRHD LTYIMLGKIF LLKGDLDKAI EIYKKAVEFS PENTELLTTL GLLYLQLGIY QKAFEHLGNT LTYDPTNYKA IL AAGSMMQ THGDFDVALT KYKVVACAVI ESPPLWNNIG MCFFGKKKYV AAISCLKRAN YLAPLDWKIL YNLGLVHLTM QQY ASAFHF LSAAINFQPK MGELYMLLAV ALTNLEDSEN AKRAYEEAVR LDKCNPLVNL NYAVLLYNQG EKRDALAQYQ EMEK KVNLL KYSSSLEFDP EMVEVAQKLG AALQVGEALV WTKPVKDPKS KHQTASTSKA AGFQQPLGSN QALGQAMSSA ATCRK LSSG AGGTSQLTKP PSLPLEPEPT VEAQPTEASA QTREK

UniProtKB: Bardet-Biedl syndrome 4 protein homolog

-
Macromolecule #4: Bardet-Biedl syndrome 5 protein homolog

MacromoleculeName: Bardet-Biedl syndrome 5 protein homolog / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 38.880984 KDa
SequenceString: MSVLDALWED RDVRFDVSSQ QMKTRPGEVL IDCLDSVEDT KGNNGDRGRL LVTNLRIVWH SLALPRVNLS IGYNCILNIT TRTANSKLR GQTEALYVLT KCNSTRFEFI FTNLVPGSPR LYTSLIAVHR AYETSKMYRD FKLRSALIQN KQLRLLPQEN V YNKINGVW ...String:
MSVLDALWED RDVRFDVSSQ QMKTRPGEVL IDCLDSVEDT KGNNGDRGRL LVTNLRIVWH SLALPRVNLS IGYNCILNIT TRTANSKLR GQTEALYVLT KCNSTRFEFI FTNLVPGSPR LYTSLIAVHR AYETSKMYRD FKLRSALIQN KQLRLLPQEN V YNKINGVW NLSSDQGNLG TFFITNVRIV WHANMNDSFN VSIPYLQIRS VKIRDSKFGL ALVIESSQQS GGYVLGFKID PV EKLQESV KEINSLHKVY SANPIFGVDY EMEEKPQPLE ALTVKQIQDD VEIDSDDHTD AFVAYFADGN KQQDREPVFS EEL GLAIEK LKDGFTLQGL WEVMN

UniProtKB: Bardet-Biedl syndrome 5 protein homolog

-
Macromolecule #5: Bardet-Biedl syndrome 7 protein homolog

MacromoleculeName: Bardet-Biedl syndrome 7 protein homolog / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 80.471375 KDa
SequenceString: MDLNLNRADY LQVGVTSQKT MKLLPASKHR ATQKVVVGDH DGIVMCFGMK KGEAVTVFKT LPGQKIARLE LGGALNTPQE KIFIAAGSE IRGFTKRGKQ FLSFETNLTE SIKAMHISGS DLFLSASYIY NHYCDCKDQH YYLSGDKIND VICLPVERLL R EVPVLACQ ...String:
MDLNLNRADY LQVGVTSQKT MKLLPASKHR ATQKVVVGDH DGIVMCFGMK KGEAVTVFKT LPGQKIARLE LGGALNTPQE KIFIAAGSE IRGFTKRGKQ FLSFETNLTE SIKAMHISGS DLFLSASYIY NHYCDCKDQH YYLSGDKIND VICLPVERLL R EVPVLACQ DRVLRVLQGS DVTYEIEVPG PPTVLALHNG NGGDSGEDLL FGTSDGKLGL IQITTSKPIH KWEIRNEKKR GG ILCVDSF DIVGDGVKDL LVGRDDGMVE VYGFDNANEP VLRFDHTLSE SVTSIQGGCV GKDGYDEIVV STYSGWITGL TTE PVHKES GPGEELKFNQ EMQNKISSLR SELEQLQYKV LQEREKYQQS SQSSKAKSAV PSFSVNDKFT LNKDDASYSL ILEV QTAID NVLIQSDVPI DLLDVDKNSA VVSFSSCDSE SNDNFLLATY RCQANTTRLE LKIRSIEGQY GTLQAYVTPR IQPKT CQVR QYHIKPLSLH QRTHFIDHDR PMNTLTLTGQ FSFSELHSWV VFCMPEVPEK PPAGECVTFY FQNTFLDTQL ESTYRK GEG VFKSDNISTI SILKDVLSKE ATKRKINLNI SYEINEVSVK HTLKLIHPKL EYQLLLAKKV QLIDALKELQ VHEGNTN FL IPEYRCILEE ADHLQEEYKK QPAHLERLYG MITDLFIDKF KFKGTNVKTK VPLLLEILDS YDQNALIAFF DAA

UniProtKB: Bardet-Biedl syndrome 7 protein homolog

-
Macromolecule #6: Tetratricopeptide repeat domain 8

MacromoleculeName: Tetratricopeptide repeat domain 8 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 56.686406 KDa
SequenceString: MEPLLLAWSY FRRRRFQLCA DLCTQMLEKS PCDQAAWILK ARALTEMVYV DEIDVDEEGI AEMILDENAI AQVPRPGTSL KLPGTNQTG GPSPAVRPVT QAGRPITGFL RPSTQSGRPG TIEQAIKTPR TAYTARPIAS SSGRFVRLGT ASMLTSPDGP F INLSRLNL ...String:
MEPLLLAWSY FRRRRFQLCA DLCTQMLEKS PCDQAAWILK ARALTEMVYV DEIDVDEEGI AEMILDENAI AQVPRPGTSL KLPGTNQTG GPSPAVRPVT QAGRPITGFL RPSTQSGRPG TIEQAIKTPR TAYTARPIAS SSGRFVRLGT ASMLTSPDGP F INLSRLNL AKYAQKPKLA KALFEYIFHH ENDVKTALDL AALSTEHSQY KDWWWKVQIG KCYYRLGLYR EAEKQFKSAL KQ QEMVDTF LYLAKVYISL DQPLTALNLF KQGLDKFPGE VTLLCGIARI YEEMNNISSA TEYYKEVLKQ DNTHVEAIAC IGS NHFYTD QPEVALRFYR RLLQMGVYNC QLFNNLGLCC FYAQQYDMTL TSFERALSLA ENEEEVADVW YNLGHVAVGT GDTN LAHQC FRLALVSNNQ HAEAYNNLAV LEMRRGHVEQ AKALLQTASS LAPHMYEPHF NFATISDKIG DLQRSYAAAK KSEAA FPDH VDTQHLIKQL EQHFAML

UniProtKB: Tetratricopeptide repeat domain 8

-
Macromolecule #7: Bardet-Biedl syndrome 9

MacromoleculeName: Bardet-Biedl syndrome 9 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 99.230914 KDa
SequenceString: MSLFKARDWW STVLGDKEEF DQGCLCLADV DNTGNGQDKI IVGSFMGYLR IFNPHPVKTG DGAQAEDLLL EVHLRDPILQ VEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN QYQIKLMYEH NLQRTACNMT YGSFGGVKGR DLICIQSVDG M LMVFEQES ...String:
MSLFKARDWW STVLGDKEEF DQGCLCLADV DNTGNGQDKI IVGSFMGYLR IFNPHPVKTG DGAQAEDLLL EVHLRDPILQ VEVGKFVSG TEMLHLAVLH SRKLCVYSVS GTLGNVEHGN QYQIKLMYEH NLQRTACNMT YGSFGGVKGR DLICIQSVDG M LMVFEQES YAFGRFLPGS LLPGPLAYSS RTDSFITVSS CHQVESYKYQ VLAFATDADK RQETEQQKHG SGKRLVVDWT LN IGEQAID ICIVSFIQSA SSVFVLGERN FFCLKDNGQI QFMKKLDYSP SCFLPYCSVS EGTINTLIGN HNNMLHIYQD VTL KWATQL PHVPVAVRVG CLHDLKGVIV TLSDDGHLQC SYLGTDPSLF QAPKVESREL NYDELDMELK ELQKVIKNVN KSQD VWPLT EREDDLKVSA MVSPNFDSVS QATDVEVGAD LVPSVTVKVT LKNRVALQKI KLSIYVQPPL VLTGDQFTFE FMAPE MTRT VGFSVYLKGS YSPPELEGNA VVSYSRPTER NPDGIPRVSQ CKFRLPLKLV CLPGQPSKTA SHKLTIDTNK SPVSLL SLF PGFAKQSEDD QVNVMGFRFL GGSQVTLLAS KTSQRYRIQS EQFEDLWLIT NELIIRLQEY FEKQGIKDFT CSFSGSV PL EEYFELIDHH FELRINGEKL EELLSERAVQ FRAIQRRLLT RFKDKTPAPL QHLDTLLDGT YKQVIALADA VEENQDNL F QSFTRLKSAT HLVILLIGLW QKLSADQIAI LEAAFLPLQQ DTQELGWEET VDAALSHLLK TCLSKSSKEQ ALNLNSQLG IPKDTSQLKK HITLFCDRLA KGGRLCLSTD AAAPQTMVMP GGCATIPESD LEGRSIDQDS SELFTNHKHL MVETPVPEVS PLQGVTE

UniProtKB: Bardet-Biedl syndrome 9

-
Macromolecule #8: BBS1 domain-containing protein

MacromoleculeName: BBS1 domain-containing protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: retina
Molecular weightTheoretical: 64.939141 KDa
SequenceString: MAATSSSDSD GGKGESEANS KWLDSLSDSM ANIHTFSACL ALADFHGDGE YKLAMGDLGP DGRQPRLKVL KGHTLVSQKP LPDLPAAAV TFLMASHEPR TPALAIASGP CVYVYKNLKP YFKFSLPSLP TNPLEQDLWN QAKEDQIDPL TLKEMLEGIR E KAEVPLSV ...String:
MAATSSSDSD GGKGESEANS KWLDSLSDSM ANIHTFSACL ALADFHGDGE YKLAMGDLGP DGRQPRLKVL KGHTLVSQKP LPDLPAAAV TFLMASHEPR TPALAIASGP CVYVYKNLKP YFKFSLPSLP TNPLEQDLWN QAKEDQIDPL TLKEMLEGIR E KAEVPLSV QSLRFLPLEL SEMEAFVNQH KSKSIRRQTV ITTMTTLKKN LADEDAVSCL VLGTENKELL VLDPEAFTIL AK MSLPSVP AFLEASGQFD VEFRLAAACR NGSIYILRRD SKRPKYCIEL GAQPVGLVGV HKVLVVGSNQ DSLHGFTYKG KRL WTVQMP AAILAMNLLE QHSRGLQAVM AALANEEVRI YHDKVLLNVI RTPEAVTSLC FGRYGREDNT LIMTTLGGGL IIKI LKRTA VFAEGGGEAG PPPSQAIKLN VPRKTRLYVD QTLREREAGT AMHRTFQADL YLLRLRAARA YVQALESSLS PVSLT AREP LKLHAVVQGL GPTFKLTLHL QNTSTARPIL GLVVCFLYNE VLYALPRAFF KVPLLVPGLN YPLETFVKSL SDKGIS DII KVLVLREGQS TPLLSAHINM PMSEGLAAD

UniProtKB: Bardet-Biedl syndrome 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloridesodium chloride
0.7 mMMgCl2Magnesium chloride
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time 20s, blot force -2, blot time 3.5s.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7839

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 560777

+
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