[English] 日本語
Yorodumi
- EMDB-21226: Negative stain reconstruction of the yeast exocyst octameric complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21226
TitleNegative stain reconstruction of the yeast exocyst octameric complex.
Map dataPurified yeast exocyst complex stained with uranyl acetate and reconstructed in Relion and cryoSPARC.Fitted PDBs are equivalent to PDB:5YFP and based on DOI: 10.2210/pdb5YFP/pdb.
Sample
  • Complex: NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX
    • Protein or peptide: Exocyst complex component SEC3Exocyst
    • Protein or peptide: Exocyst complex component SEC5Exocyst
    • Protein or peptide: Exocyst complex component SEC6Exocyst
    • Protein or peptide: Exocyst complex component SEC8Exocyst
    • Protein or peptide: Exocyst complex component SEC10Exocyst
    • Protein or peptide: Exocyst complex component SEC15Exocyst
    • Protein or peptide: Exocyst complex component EXO70Exocyst
    • Protein or peptide: Exocyst complex component EXO84Exocyst
KeywordsEXOCYST / COILED-COIL / EXOCYTOSIS
Function / homology
Function and homology information


vesicle tethering involved in exocytosis / exocyst assembly / exocyst localization / negative regulation of SNARE complex assembly / Insulin processing / endoplasmic reticulum inheritance / exocyst / prospore membrane / Golgi inheritance / incipient cellular bud site ...vesicle tethering involved in exocytosis / exocyst assembly / exocyst localization / negative regulation of SNARE complex assembly / Insulin processing / endoplasmic reticulum inheritance / exocyst / prospore membrane / Golgi inheritance / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / spliceosomal complex assembly / exocytosis / Rho protein signal transduction / transport vesicle / phosphatidylinositol-4,5-bisphosphate binding / SNARE binding / cell periphery / intracellular protein transport / protein localization / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
Exocyst complex subunit Sec15, C-terminal / : / : / : / : / Exocyst complex component EXOC6/Sec15, N-terminal / Exocyst complex component Sec8 C-terminal / Exocyst complex component Sec10, N-terminal / Exocyst complex component EXOC6/Sec15 / Exocyst complex component Sec10-like ...Exocyst complex subunit Sec15, C-terminal / : / : / : / : / Exocyst complex component EXOC6/Sec15, N-terminal / Exocyst complex component Sec8 C-terminal / Exocyst complex component Sec10, N-terminal / Exocyst complex component EXOC6/Sec15 / Exocyst complex component Sec10-like / Exocyst complex component EXOC6/Sec15, C-terminal, domain 1 / Exocyst complex component EXOC3/Sec6, C-terminal domain / Exocyst complex subunit Sec15 C-terminal / Exocyst complex component Sec10-like, alpha-helical bundle / Exocyst complex component Sec8, N-terminal / Exocyst complex component EXOC3/Sec6 / Exocyst complex component EXOC2/Sec5 / Exocyst complex component EXOC2/Sec5, N-terminal domain / Exocyst complex component Sec8/EXOC4 / Exocyst complex component Sec8 N-terminal / Exocyst complex component Sec6 / Exocyst complex component Sec5 / Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Vps51/EXO84/COG1 N-terminal / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Exo70 / EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2 / Exo70 exocyst complex subunit C-terminal / Cullin repeat-like-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Exocyst complex component EXO70 / Exocyst complex component SEC15 / Exocyst complex component SEC6 / Exocyst complex component SEC8 / Exocyst complex component SEC3 / Exocyst complex component EXO84 / Exocyst complex component SEC5 / Exocyst complex component SEC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsFrost A / Munson M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R01GM068803 United States
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Subunit connectivity, assembly determinants and architecture of the yeast exocyst complex.
Authors: Margaret R Heider / Mingyu Gu / Caroline M Duffy / Anne M Mirza / Laura L Marcotte / Alexandra C Walls / Nicholas Farrall / Zhanna Hakhverdyan / Mark C Field / Michael P Rout / Adam Frost / Mary Munson /
Abstract: The exocyst is a hetero-octameric complex that has been proposed to serve as the tethering complex for exocytosis, although it remains poorly understood at the molecular level. Here, we purified ...The exocyst is a hetero-octameric complex that has been proposed to serve as the tethering complex for exocytosis, although it remains poorly understood at the molecular level. Here, we purified endogenous exocyst complexes from Saccharomyces cerevisiae and showed that they are stable and consist of all eight subunits with equal stoichiometry. Using a combination of biochemical and auxin induced-degradation experiments in yeast, we mapped the subunit connectivity, identified two stable four-subunit modules within the octamer and demonstrated that several known exocyst-binding partners are not necessary for exocyst assembly and stability. Furthermore, we visualized the structure of the yeast complex by using negative-stain electron microscopy; our results indicate that the exocyst exists predominantly as a stable, octameric complex with an elongated architecture that suggests that the subunits are contiguous helical bundles packed together into a bundle of long rods.
History
DepositionJan 21, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 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: 4.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vkl
  • Surface level: 4.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21226.png

Downloads & links

-
Map

FileDownload / File: emd_21226.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPurified yeast exocyst complex stained with uranyl acetate and reconstructed in Relion and cryoSPARC.Fitted PDBs are equivalent to PDB:5YFP and based on DOI: 10.2210/pdb5YFP/pdb.
Voxel sizeX=Y=Z: 2.871 Å
Density
Contour LevelBy AUTHOR: 4.1 / Movie #1: 4.1
Minimum - Maximum-2.171029 - 11.401691
Average (Standard dev.)0.028356869 (±0.40476105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 734.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.8712.8712.871
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z734.976734.976734.976
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.17111.4020.028

-
Supplemental data

-
Sample components

-
Entire : NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX

EntireName: NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX
Components
  • Complex: NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX
    • Protein or peptide: Exocyst complex component SEC3Exocyst
    • Protein or peptide: Exocyst complex component SEC5Exocyst
    • Protein or peptide: Exocyst complex component SEC6Exocyst
    • Protein or peptide: Exocyst complex component SEC8Exocyst
    • Protein or peptide: Exocyst complex component SEC10Exocyst
    • Protein or peptide: Exocyst complex component SEC15Exocyst
    • Protein or peptide: Exocyst complex component EXO70Exocyst
    • Protein or peptide: Exocyst complex component EXO84Exocyst

-
Supramolecule #1: NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX

SupramoleculeName: NEGATIVE STAIN MAP OF THE YEAST EXOCYST COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Exocyst complex component SEC3

MacromoleculeName: Exocyst complex component SEC3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 154.889547 KDa
SequenceString: MRSSKSPFKR KSHSRETSHD ENTSFFHKRT ISGSSAHHSR NVSQGAVPSS APPVSGGNYS HKRNVSRASN SSQTSNFLAE QYERDRKAI INCCFSRPDH KTGEPPNNYI THVRIIEDSK FPSSRPPPDS KLENKKKRLL ILSAKPNNAK LIQIHKAREN S DGSFQIGR ...String:
MRSSKSPFKR KSHSRETSHD ENTSFFHKRT ISGSSAHHSR NVSQGAVPSS APPVSGGNYS HKRNVSRASN SSQTSNFLAE QYERDRKAI INCCFSRPDH KTGEPPNNYI THVRIIEDSK FPSSRPPPDS KLENKKKRLL ILSAKPNNAK LIQIHKAREN S DGSFQIGR TWQLTELVRV EKDLEISEGF ILTMSKKYYW ETNSAKERTV FIKSLITLYI QTFEGHVPEL VNWDLSLFYL DE RSYQRAV ITNRPGSVSP IKSPTSNFTT NTTQSVGSVP FSAPTERTRR SETESVNPVS TPASVEYHAG MKSLNKAPYS SNS TLNEVN KRYELEQQQQ QEEAELRRLE EQKRLQLQKE NEMKRLEEER RIKQEERKRQ MELEHQRQLE EEERKRQMEL EAKK QMELK RQRQFEEEQR LKKERELLEI QRKQREQETA ERLKKEEQEA LAKKEEEEKS KRNKVDNESY TQEINGKVDN LLEDL NAVL AEETETTPTM QNGTYVPERS TARAHDQLKK PLNIAKVESL GGSDLNDSIS LSDEIAGLNT SNLSGEDQDE KNDLSF EKG DEVRYSNNFE GEAPHVYHEV SIIQEEAPAV SQKLILPEEN NESEALIESK EEIKTMENID DEVLLEILTD INWSIED DA DSMIERIDLR LAETEYLFNQ NLLSLQKIGP NIRPYEDKVN DECHRIIPTL SLFLMEMSNF SNDIENVESQ DNGLQVES A NKKLLWNTLD ELLKTVSLDE ISLNQLLECP IREKNLPWME NQLNLLLKAF QAIGSDGNEV EYNLREISGL KQRLQFYEK VTKIFLNRIV EEMQKKFSNI RGQDISHDQM IRILTTLLIF SPLILFCKEI SQKSYQAIVE NWNVSIQPVY MELWTKKISQ LQGIDTNDE KMNELSLSQL LNEWDTFRKE RKTNDINPVF KNSFSLLTEC LQTMRQECIV YQNFVEVFFH ISSKHNFEEY I KHFNDPDA PPILLDTVKV MQSDREAAVI ETQLVSRIFQ PIVTRLSSYF VELVKAEPTV APALTFYLEN EIKSLESSNH EF LLSAVTR MYTQIKQVWS DNVEEQVLHF ERISNATTNG EILPGILDLP VGLKNSEDLF QFAKRSMDIK DTDEGYESIE LMN SSFRKL SIAATRSITH KEVNSSINPN LSDTAALNND YMETISLLVN SNWLTEMLSM LNFNKDGIFD TSLQNVKKVF DVEK ESYAS FLLRDTMPKL TAFVYGVSNI IENTNNVNMT NPSRWAAYSR QNLENILLAY TSHEIETLVK RLHTHMVNDF GYHQE NAIN NVLCDKLWSC IQGQTVSLYL KLYTVIDKHY RGTNIRFTKN DIISAFEEYK NA

UniProtKB: Exocyst complex component SEC3

-
Macromolecule #2: Exocyst complex component SEC5

MacromoleculeName: Exocyst complex component SEC5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 112.236875 KDa
SequenceString: MDRFQIGDEQ LLRFYQLKTI NPTHSWAQDS SKLNNEEATS NELGVETSFD ILKDFKYGNQ ISIDKESRAY LNDESLSYIR DPLNGQEMS KELQHLPNDS MRLNYLVNSK QFNVKAFLRD MHKQDSFNDL NNSLDRLDSD IQDQSIHLKQ LVGKNFTKYV K IKNKLDQI ...String:
MDRFQIGDEQ LLRFYQLKTI NPTHSWAQDS SKLNNEEATS NELGVETSFD ILKDFKYGNQ ISIDKESRAY LNDESLSYIR DPLNGQEMS KELQHLPNDS MRLNYLVNSK QFNVKAFLRD MHKQDSFNDL NNSLDRLDSD IQDQSIHLKQ LVGKNFTKYV K IKNKLDQI YKEFDEKTNE KNQCDSPKEN QINVESLNKK VDEVIRTTTF KLKPLMDNYQ KILNYQATKK FIELNKFYFN LP KSLKRCL TNNDFNEFII EYSKGLTLRR RFNQSSDASQ SLVIKRIWTQ IENLLVTYKD LIWNSLINSN FNIDQPQETI LSL FSKLLN LENFINNNQR ESESGNKNTT SSSNENPILR WMSIKMNGFQ NELNELSGHM ISKIIHSQRL ILQNNTNQDK SQGC VELSY YLKINQLFQI ISDTGKDSEG LKSTVEPNKV NTISGTSYLN LNCQPSSQGL TDSPTIIEMW LLILKYINDL WKICD QFIE FWEHIEKFLD GTYQNSIINE KRKENILIGD SNIIESYQKS LILKEEQINE VRLKGEEFIT SVSQNLISFF TSSQSS LPS SLKDSTGDIT RSNKDSGSPL DYGFIPPNCN GLSCLRYLPK IVEPILKFST ELAQLNITTN GITICRNTLS TIINRCV GA ISSTKLRDIS NFYQLENWQV YETVTFSSKS QDSSKNLTFE YGVTQFPEIV TSFQEVSIKT TRDLLFAYEK LPIINGIS V VSYPSKQLLT GIEIQQIISM EAVLEAILKN AAKDKDNPRN SHTILTLTNL QYFRECAFPN ILQYFDDAFE WNLASKNLE LFSLLSKMES SIFGNYLSDL KINLRDTLEE KFHEINWPMY TSNSFRVGDY IIEALMILIV VHSECFRIGP QLIHKILIET QIFIARYLF EAFKPYVGNL SNDGSLQIIV DLEFFQKVMG PLLEKDTEAT LRACLQNCFQ NDTNRLQKCI NEINPIVSAN L KRTAIQFA AFS

UniProtKB: Exocyst complex component SEC5

-
Macromolecule #3: Exocyst complex component SEC6

MacromoleculeName: Exocyst complex component SEC6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 93.539703 KDa
SequenceString: MSSDPLQQVC DLIKGDLSLE RVRDIKEQLL KEKSVVEYQL NKESDKYYGE VEESLKLLNL SKNSVTSIKQ QINEVNKLGN DNRFAINRY DILFRATKLY ETVNTTSSIY DRIYNFVALM EHIERLLVAE LAEDALETGC PHLLEIHFLL TSARDFQEQV V VMAKEATE ...String:
MSSDPLQQVC DLIKGDLSLE RVRDIKEQLL KEKSVVEYQL NKESDKYYGE VEESLKLLNL SKNSVTSIKQ QINEVNKLGN DNRFAINRY DILFRATKLY ETVNTTSSIY DRIYNFVALM EHIERLLVAE LAEDALETGC PHLLEIHFLL TSARDFQEQV V VMAKEATE DAQRTVMKLF SRLSGIISKF DKLLDGLTYD IVEMARAEQI SLAIRLFKIY DLEEREDLRI EAIRNIIKKK EI EIEKSSI KKLPNSKNTA RLQDETPKVI EYPTNKGLYQ EIMSGTISTR TAPRGYKHFL INGINNSISE MFGEMREKYV GDQ KFDVLD NMDWIFNELI IVKEHIANCC PPHWNIFEVY FDQYYKELHS LITDLVESEP ETIIILDILA FDKTFQDTLK QDFG FTKSE VKSVIGDKEK ETLFKDYLNL IVVKMTEWIG NLEKAEFDVF LERSTPPHSD SDGLLFLDGT KTCFQMFTQQ VEVAA GTNQ AKILVGVVER FSDLLTKRQK NWISKISEEI KKQINYNHKY DIDPESITPE DECPGGLVEY LIAVSNDQMK AADYAV AIS SKYGKLVSKV YEKQITNHLE GTLDGFAEVA QCSSLGLITL MFDDLRKPYQ EIFSKTWYMG SQAQQIADTL DEYLLDI KP QMNSVLFVNF IDNVIGETII KFLTALSFEH SFKNKNNKFL EAMKRDFEIF YQLFVKVLDG NESKDTLITQ NFTVMEFF M DLSCEPIDSI LDIWQKYLEV YWDSRIDLLV GILKCRKDVS SSERKKIVQQ ATEMLHEYRR NMEANGVDRE PTLMRRFVL EFEKQ

UniProtKB: Exocyst complex component SEC6

-
Macromolecule #4: Exocyst complex component SEC8

MacromoleculeName: Exocyst complex component SEC8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 122.367109 KDa
SequenceString: MDYLKPAQKG RRRGLSINSL SETQQSAMNS SLDHLQNDLN RINLQWNRIL SDNTNPLELA LAFLDDTSVG LGHRYEEFNQ LKSQIGSHL QDVVNEHSQV FNTNVASYGK AVSSIMQAQE QTLNLKNCLK EANEKITTDK GSLQELNDNN LKYTKMIDVL V NIEELLQI ...String:
MDYLKPAQKG RRRGLSINSL SETQQSAMNS SLDHLQNDLN RINLQWNRIL SDNTNPLELA LAFLDDTSVG LGHRYEEFNQ LKSQIGSHL QDVVNEHSQV FNTNVASYGK AVSSIMQAQE QTLNLKNCLK EANEKITTDK GSLQELNDNN LKYTKMIDVL V NIEELLQI PEKIEENIRK ENFHQVQILL ERGFILMNNK SLKTVEILKP INQQLELQEH LLFNNLIEEI HDIMYSKSNK TN FTRVTNN DIFKIISISH NGFTSLENYL YNIVNIDIME HSKTINKNLE QFIHDQSLNK GNIMLQENAA TQAPLAPSRN QEN EGFNRI GFLLKTINNI NKLPVAFNII TERAKEEIHN IIVKSTESIR SKHPSLLKMA TSLKNDNHFG LPVQDILSII LREC FWEIF LKLLYAIQCH RAIFEMSNIL QPTSSAKPAF KFNKIWGKLL DEIELLLVRY INDPELISSN NGSIKPINGA TNNAP TLPK RKNPKIFSLE YNIEDNSSVK DQAFELKALL KDIFPGFSVS SNMDLDSIYV KDESFEQDEP LVPPSVFNMK VILDPF LLF TQSTSTIVPS VLTQNTISSL TFFDDYMNKS FLPKIQMTMD YLFTVEVESN NPYALELSDE NHNIFKTALD FQRLFYN LL NVFNTANTFR EKISYCILDL LNHFYNYYLG LFNSLIGTSD RHLTRKIITA WLQNGILMDQ EQKILNGDET LFHEESIE L FKEIPHFYQA GKGLSKSDLF NNLTLDTILQ FSASVLWILN WLPGLKKAIN IDEVSQEPML DADRLRSSWT FSESMDLNY SNPSSSPNSL GNLKILLDDK ASKKFDETID GFKTLKFKLI TILRFNIRAL CIYDIGSFFQ NTKIWNMDVG SIELDQNIAS LISELRRTE SKLKQQLPEK EKNSIFIGLD IVNNYALIKG AKSIKVLNHN GIKKMLRNVN VLQHAYRNLS SEPSKINMNV T MNFYSLCG SSEAELFEYI KDNELPHCSV EDLKTILRLQ FSEEMHRQLK RQSTSSTKGS IKPSNKRYTE ALEKLSNLEK EQ SKEGART KIGKLKSKLN AVHTANEK

UniProtKB: Exocyst complex component SEC8

-
Macromolecule #5: Exocyst complex component SEC10

MacromoleculeName: Exocyst complex component SEC10 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.459578 KDa
SequenceString: MNSLYELDPK WKKLLKTDNF LGGLTVNEFV QELSKDHRND VLIDANTKNL PTNEKDQDAI REAIWKQLDP KPYIRTFEST LKELKNLNE ETLNKRQYFS EQVATQEVIH SENVIKLSKD LHTTLLTFDK LDDRLTNVTQ VVSPLGDKLE TAIKKKQNYI Q SVELIRRY ...String:
MNSLYELDPK WKKLLKTDNF LGGLTVNEFV QELSKDHRND VLIDANTKNL PTNEKDQDAI REAIWKQLDP KPYIRTFEST LKELKNLNE ETLNKRQYFS EQVATQEVIH SENVIKLSKD LHTTLLTFDK LDDRLTNVTQ VVSPLGDKLE TAIKKKQNYI Q SVELIRRY NDFYSMGKSD IVEQLRLSKN WKLNLKSVKL MKNLLILSSK LETSSIPKTI NTKLVIEKYS EMMENELLEN FN SAYRENN FTKLNEIAII LNNFNGGVNV IQSFINQHDY FIDTKQIDLE NEFENVFIKN VKFKEQLIDF ENHSVIIETS MQN LINDVE TVIKNESKIV KRVFEEKATH VIQLFIQRVF AQKIEPRFEV LLRNSLSISN LAYVRILHGL FTLFGKFTKS LIDY FQLLE IDDSNQILST TLEQCFADLF SHYLYDRSKY FGIEKRSLEA ILVDMTSKFT VNYDKEINKR VLLDKYKEKL STNVD AFMH SPRGNTHSRQ DSTSRSKLSQ FNSFLKTHLD KDHLSLNRTN TLSDSFNNSS SSTQYDVANN SSSLVNSSFT ASDIDN SPN SPANYSLNDV DSMLKCVVES TARVMELIPN KAHLYILEIL KIMFLGIVDS YMEIALEVAY WKICKVDINK TAGVVNL NF LKFISMSTEI LDLLSISIKS IFLPLLNNSP EIKAQIIEMT NSQIQKMEIL INIILQETIT VISTKFSAIL CKQKKKDF V PKSQELLDQD TLPAIEIVNI LNLIFEQSSK FLKGKNLQTF LTLIGEELYG LLLSHYSHFQ VNSIGGVVVT KDIIGYQTA IEDWGVASLI DKFATLRELA NLFTVQPELL ESLTKEGHLA DIGRDIIQSY ISNREDFNHD NFINSVKLNF R

UniProtKB: Exocyst complex component SEC10

-
Macromolecule #6: Exocyst complex component SEC15

MacromoleculeName: Exocyst complex component SEC15 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 105.166641 KDa
SequenceString: MDQEGQPLLS KDFQQVLLAT ASGNNSSWTE RAVLNNESTD AVKHEPALGQ NDVFDLDPLS FDKWVPFLRR ALDKNQLDPV IDELENSIE DNFQGLELQL LQDSQMNDKL ETSIDEIANI QGMVQDTLSS EISKFQIRLS ESANELIVKK QMYVNNKKIS L KISEATIL ...String:
MDQEGQPLLS KDFQQVLLAT ASGNNSSWTE RAVLNNESTD AVKHEPALGQ NDVFDLDPLS FDKWVPFLRR ALDKNQLDPV IDELENSIE DNFQGLELQL LQDSQMNDKL ETSIDEIANI QGMVQDTLSS EISKFQIRLS ESANELIVKK QMYVNNKKIS L KISEATIL ITKVVRILEL SSKCQELITE RKFFKVLQNL DSLEKLYLQE FKNYNFQFLI EIYNSIPFLQ KVTKDECINL IR NSLNLNL GKNLIKVGQE FVAIYENELL PQWLETRSKM KLTNFKFNSP IEISMRDESF LAKLNLGEFF QLDDFHDSIM IFQ NLNELS VLSGEFNKEY ELRKTKLMYP LIWKKNKTAA YQMDSLLRGT GTTPGSTAHD VSTDDPFTQS LSLHFLQDYF LKIL GFLLY DINLNKATEF ILVDNNYNST NEFWDGLMDR LSPYLSYFID EKLKTEEDMI KLKDFLCIYV AILENFKLNI EPLYK ILVS IFEKFCSVSL RAFDDEFQIL LNDDDFMPLS INDKTLYEKV LKICWMKEGE HLSLPDPTNG EPFAVTLPFS PLYPMT CTL AKKTYSKITA FLSIFYRHEL HTLNNILVKT MDDIFNDIVN KKIRSKLEST SREEIAQILV NLDYFIIAAK EFSNFMT RE NILQNPDMEI RLSSIKYLAE SRKLAETKLI ELIDSKISDI LETIEIDWQI TEVRQDPDIS IIDLAQFLEM MFASTLQN L PYSVQTLLIF REFDSLTRQF MGLLLHDTPS TITHESIMNF EVDVNYLESI IPRIFPSTPG TIDSNGYQSP MTPSTPTFP NANGVDAPTL FENNIKSLEA TFMELKQCIE LLKTQGKDYN EPEIRLRKYS RIRQEDAALL LSKIQHFVSS VEGANGDDTS VMDSSSIFN SESASVIDSN TSRIAKFFNR R

UniProtKB: Exocyst complex component SEC15

-
Macromolecule #7: Exocyst complex component EXO70

MacromoleculeName: Exocyst complex component EXO70 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 71.382328 KDa
SequenceString: MPAEIDIDEA DVLVLSQELQ KTSKLTFEIN KSLKKIAATS NQSSQLFTPI LARNNVLTTL QRNIESTLNS VASVKDLANE ASKYEIILQ KGINQVGLKQ YTQVVHKLDD MLEDIQSGQA NREENSEFHG ILTHLEQLIK RSEAQLRVYF ISILNSIKPF D PQINITKK ...String:
MPAEIDIDEA DVLVLSQELQ KTSKLTFEIN KSLKKIAATS NQSSQLFTPI LARNNVLTTL QRNIESTLNS VASVKDLANE ASKYEIILQ KGINQVGLKQ YTQVVHKLDD MLEDIQSGQA NREENSEFHG ILTHLEQLIK RSEAQLRVYF ISILNSIKPF D PQINITKK MPFPYYEDQQ LGALSWILDY FHGNSEGSII QDILVGERSK LILKCMAFLE PFAKEISTAK NAPYEKGSSG MN SYTEALL GFIANEKSLV DDLYSQYTES KPHVLSQILS PLISAYAKLF GANLKIVRSN LENFGFFSFE LVESINDVKK SLR GKELQN YNLLQDCTQE VRQVTQSLFR DAIDRIIKKA NSISTIPSNN GVTEATVDTM SRLRKFSEYK NGCLGAMDNI TREN WLPSN YKEKEYTLQN EALNWEDHNV LLSCFISDCI DTLAVNLERK AQIALMPNQE PDVANPNSSK NKHKQRIGFF ILMNL TLVE QIVEKSELNL MLAGEGHSRL ERLKKRYISY MVSDWRDLTA NLMDSVFIDS SGKKSKDKEQ IKEKFRKFNE GFEDLV SKT KQYKLSDPSL KVTLKSEIIS LVMPMYERFY SRYKDSFKNP RKHIKYTPDE LTTVLNQLVR

UniProtKB: Exocyst complex component EXO70

-
Macromolecule #8: Exocyst complex component EXO84

MacromoleculeName: Exocyst complex component EXO84 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 85.649672 KDa
SequenceString: MVEFSLKKAR NNWKHVKKSA SSPAKQKTPP SPAKPKQKTK KNPYSDLKDP ATSYTLPTIN ARERSRVATS MQRRLSIHNT NYAPPTLDY SMPLPDMPNM IVPNDNVDSS HNNSSFTTEN ESVSSKGPSN SLNLSTADLS LNDSSYNKVP ARSAMRNTVN P SGSNDPFN ...String:
MVEFSLKKAR NNWKHVKKSA SSPAKQKTPP SPAKPKQKTK KNPYSDLKDP ATSYTLPTIN ARERSRVATS MQRRLSIHNT NYAPPTLDY SMPLPDMPNM IVPNDNVDSS HNNSSFTTEN ESVSSKGPSN SLNLSTADLS LNDSSYNKVP ARSAMRNTVN P SGSNDPFN NSTSLRKMLA NPHFNAKDFV HDKLGNASAI TIDKFTSNLT DLSIQVQEEV KLNINKSYNE IMTVNNDLNV AM LELKRVR ANINDLNEVL DQCTKIAEKR LQLQDQIDQE RQGNFNNVES HSNSPALLPP LKAGQNGNLM RRDRSSVLIL EKF WDTELD QLFKNVEGAQ KFINSTKGRH ILMNSANWME LNTTTGKPLQ MVQIFILNDL VLIADKSRDK QNDFIVSQCY PLKD VTVTQ EEFSTKRLLF KFSNSNSSLY ECRDADECSR LLDVIRKAKD DLCDIFHVEE ENSKRIRESF RYLQSTQQTP GRENN RSPN KNKRRSMGGS ITPGRNVTGA MDQYLLQNLT LSMHSRPRSR DMSSTAQRLK FLDEGVEEID IELARLRFES AVETLL DIE SQLEDLSERI SDEELMLLNL ISLKIEQRRE AISSKLSQSI LSSNEIVHLK SGTENMIKLG LPEQALDLFL QNRSNFI QD LILQIGSVDN PTNYLTQLAV IRFQTIKKTV EDFQDIFKEL GAKISSILVD WCSDEVDNHF KLIDKQLLND EMLSPGSI K SSRKQIDGLK AVGLDFVYKL DEFIKKNSDK IR

UniProtKB: Exocyst complex component EXO84

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.30 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified

-
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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 22500
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 6466 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing #1

Startup modelType of model: OTHER / Details: de novo model generated in cryoSPARC.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 67509
Image processing ID1

-
Image processing #2

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 67509
Image processing ID2

-
Atomic model buiding 1

Initial modelPDB ID:

5yfp


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6vkl:
Negative stain reconstruction of the yeast exocyst octameric complex.

+
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