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- EMDB-18701: Endosomal membrane tethering complex CORVET -

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Basic information

Entry
Database: EMDB / ID: EMD-18701
TitleEndosomal membrane tethering complex CORVET
Map dataCORVET composite map and associated molecular model
Sample
  • Complex: Endosomal membrane tethering complex CORVET
    • Protein or peptide: Vacuolar protein sorting-associated protein 8
    • Protein or peptide: Vacuolar protein sorting-associated protein 33
    • Protein or peptide: Vacuolar protein sorting-associated protein 16
    • Protein or peptide: E3 ubiquitin-protein ligase PEP5
    • Protein or peptide: Vacuolar protein sorting-associated protein 3
    • Protein or peptide: Vacuolar membrane protein PEP3
KeywordsCORVET / membrane fusion / endosome / Rab GTPase / tethering / ENDOCYTOSIS
Function / homology
Function and homology information


histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole inheritance / vacuole fusion, non-autophagic ...histone catabolic process / organelle fusion / endosomal vesicle fusion / regulation of SNARE complex assembly / CORVET complex / HOPS complex / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole inheritance / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / Golgi to vacuole transport / vesicle docking / late endosome to vacuole transport via multivesicular body sorting pathway / endosome organization / vacuole organization / protein targeting to vacuole / late endosome to vacuole transport / piecemeal microautophagy of the nucleus / Golgi stack / fungal-type vacuole / fungal-type vacuole membrane / vesicle docking involved in exocytosis / vacuolar acidification / endosomal transport / lysosome organization / endosome to lysosome transport / protein-membrane adaptor activity / vesicle-mediated transport / intracellular protein transport / RING-type E3 ubiquitin transferase / autophagy / endocytosis / ubiquitin protein ligase activity / late endosome / GTPase binding / protein-macromolecule adaptor activity / actin binding / early endosome membrane / endosome / ATP binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 8, central domain / Golgi CORVET complex core vacuolar protein 8 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain / Vacuolar protein sorting protein 11 C terminal / Vam6/VPS39/TRAP1 family / Vps16, C-terminal ...Vacuolar protein sorting-associated protein 8, central domain / Golgi CORVET complex core vacuolar protein 8 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Pep3/Vps18/deep orange / Vacuolar protein sorting-associated protein 11 / Vacuolar protein sorting protein 11, C-terminal / Pep3/Vps18/deep orange beta-propeller domain / Vacuolar protein sorting protein 11 C terminal / Vam6/VPS39/TRAP1 family / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Ring finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase PEP5 / Vacuolar protein sorting-associated protein 33 / Vacuolar protein sorting-associated protein 3 / Vacuolar membrane protein PEP3 / Vacuolar protein sorting-associated protein 8 / Vacuolar protein sorting-associated protein 16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsShvarev D / Ungermann C / Moeller A / Langemeyer L / Walter S / Perz A / Froehlich F
Funding support Germany, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)UN111/5-6 Germany
German Research Foundation (DFG)MO2752/3-6 Germany
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)SFB 1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchDLR 01ED2010 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the endosomal CORVET tethering complex.
Authors: Dmitry Shvarev / Caroline König / Nicole Susan / Lars Langemeyer / Stefan Walter / Angela Perz / Florian Fröhlich / Christian Ungermann / Arne Moeller /
Abstract: Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion ...Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solve the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discover that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane lipid packing defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function.
History
DepositionOct 23, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18701.png

Downloads & links

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Map

FileDownload / File: emd_18701.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCORVET composite map and associated molecular model
Voxel sizeX=Y=Z: 2.037 Å
Density
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.053855367 - 1.9892938
Average (Standard dev.)0.009227127 (±0.022777678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 814.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Endosomal membrane tethering complex CORVET

EntireName: Endosomal membrane tethering complex CORVET
Components
  • Complex: Endosomal membrane tethering complex CORVET
    • Protein or peptide: Vacuolar protein sorting-associated protein 8
    • Protein or peptide: Vacuolar protein sorting-associated protein 33
    • Protein or peptide: Vacuolar protein sorting-associated protein 16
    • Protein or peptide: E3 ubiquitin-protein ligase PEP5
    • Protein or peptide: Vacuolar protein sorting-associated protein 3
    • Protein or peptide: Vacuolar membrane protein PEP3

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Supramolecule #1: Endosomal membrane tethering complex CORVET

SupramoleculeName: Endosomal membrane tethering complex CORVET / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vacuolar protein sorting-associated protein 8

MacromoleculeName: Vacuolar protein sorting-associated protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 148.102172 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MEQNGLDHDS RSSIDTTIND TQKTFLEFRS YTQLSEKLAS SSSYTAPPLN EDGPKGVASA VSQGSESVVS WTTLTHVYSI LGAYGGPTC LYPTATYFLM GTSKGCVLIF NYNEHLQTIL VPTLSEDPSI HSIRSPVKSI VICSDGTHVA ASYETGNICI W NLNVGYRV ...String:
MEQNGLDHDS RSSIDTTIND TQKTFLEFRS YTQLSEKLAS SSSYTAPPLN EDGPKGVASA VSQGSESVVS WTTLTHVYSI LGAYGGPTC LYPTATYFLM GTSKGCVLIF NYNEHLQTIL VPTLSEDPSI HSIRSPVKSI VICSDGTHVA ASYETGNICI W NLNVGYRV KPTSEPTNGM TPTPALPAVL HIDDHVNKEI TGLDFFGARH TALIVSDRTG KVSLYNGYRR GFWQLVYNSK KI LDVNSSK EKLIRSKLSP LISREKISTN LLSVLTTTHF ALILLSPHVS LMFQETVEPS VQNSLVVNSS ISWTQNCSRV AYS VNNKIS VISISSSDFN VQSASHSPEF AESILSIQWI DQLLLGVLTI SHQFLVLHPQ HDFKILLRLD FLIHDLMIPP NKYF VISRR SFYLLTNYSF KIGKFVSWSD ITLRHILKGD YLGALEFIES LLQPYCPLAN LLKLDNNTEE RTKQLMEPFY NLSLA ALRF LIKKDNADYN RVYQLLMVVV RVLQQSSKKL DSIPSLDVFL EQGLEFFELK DNAVYFEVVA NIVAQGSVTS ISPVLF RSI IDYYAKEENL KVIEDLIIML NPTTLDVDLA VKLCQKYNLF DLLIYIWNKI FDDYQTPVVD LIYRISNQSE KCVIFNG PQ VPPETTIFDY VTYILTGRQY PQNLSISPSD KCSKIQRELS AFIFSGFSIK WPSNSNHKLY ICENPEEEPA FPYFHLLL K SNPSRFLAML NEVFEASLFN DDNDMVASVG EAELVSRQYV IDLLLDAMKD TGNSDNIRVL VAIFIATSIS KYPQFIKVS NQALDCVVNT ICSSRVQGIY EISQIALESL LPYYHSRTTE NFILELKEKN FNKVLFHIYK SENKYASALS LILETKDIEK EYNTDIVSI TDYILKKCPP GSLECGKVTE VIETNFDLLL SRIGIEKCVT IFSDFDYNLH QEILEVKNEE TQQKYLDKLF S TPNINNKV DKRLRNLHIE LNCKYKSKRE MILWLNGTVL SNAESLQILD LLNQDSNFEA AAIIHERLES FNLAVRDLLS FI EQCLNEG KTNISTLLES LRRAFDDCNS AGTEKKSCWI LLITFLITLY GKYPSHDERK DLCNKLLQEA FLGLVRSKSS SQK DSGGEF WEIMSSVLEH QDVILMKVQD LKQLLLNVFN TYKLERSLSE LIQKIIEDSS QDLVQQYRKF LSEGWSIHTD DCEI CGKKI WGAGLDPLLF LAWENVQRHQ DMISVDLKTP LVIFKCHHGF HQTCLENLAQ KPDEYSCLIC QTESNPKIVD YKDDD DKDY KDDDDKDYKD DDDK

UniProtKB: Vacuolar protein sorting-associated protein 8

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Macromolecule #2: Vacuolar protein sorting-associated protein 33

MacromoleculeName: Vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 79.354977 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNRFWNTKKF SLTNADGLCA TLNEISQNDE VLVVQPSVLP VLNSLLTFQD LTQSTPVRKI TLLDDQLSDD LPSALGSVPQ MDLIFLIDV RTSLRLPPQL LDAAQKHNLS SLHIIYCRWK PSFQNTLEDT EQWQKDGFDL NSKKTHFPNV IESQLKELSN E YTLYPWDL ...String:
MNRFWNTKKF SLTNADGLCA TLNEISQNDE VLVVQPSVLP VLNSLLTFQD LTQSTPVRKI TLLDDQLSDD LPSALGSVPQ MDLIFLIDV RTSLRLPPQL LDAAQKHNLS SLHIIYCRWK PSFQNTLEDT EQWQKDGFDL NSKKTHFPNV IESQLKELSN E YTLYPWDL LPFPQIDENV LLTHSLYNME NVNMYYPNLR SLQSATESIL VDDMVNSLQS LIFETNSIIT NVVSIGNLSK RC SHLLKKR IDEHQTENDL FIKGTLYGER TNCGLEMDLI ILERNTDPIT PLLTQLTYAG ILDDLYEFNS GIKIKEKDMN FNY KEDKIW NDLKFLNFGS IGPQLNKLAK ELQTQYDTRH KAESVHEIKE FVDSLGSLQQ RQAFLKNHTT LSSDVLKVVE TEEY GSFNK ILELELEILM GNTLNNDIED IILELQYQYE VDQKKILRLI CLLSLCKNSL REKDYEYLRT FMIDSWGIEK CFQLE SLAE LGFFTSKTGK TDLHITTSKS TRLQKEYRYI SQWFNTVPIE DEHAADKITN ENDDFSEATF AYSGVVPLTM RLVQML YDR SILFHNYSSQ QPFILSREPR VSQTEDLIEQ LYGDSHAIEE SIWVPGTITK KINASIKSNN RRSIDGSNGT FHAAEDI AL VVFLGGVTMG EIAIMKHLQK ILGKKGINKR FIIIADGLIN GTRIMNSIS

UniProtKB: Vacuolar protein sorting-associated protein 33

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Macromolecule #3: Vacuolar protein sorting-associated protein 16

MacromoleculeName: Vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 92.857 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKNPSFDWER LKDVFYRSRA IGELKWPTQY EEFKCALSLT VIAVEIQDFI QVYNYFGQLL GKINLQRIHE DIIKFEFDKD EKLILVTKS SIKIVKGWSP LTIESVPLQD PTIDTIWDYH NGIMLLAKSR DIYKLNGNEW ELLYENKDKK YNLLTKNHWS C NDDSIILL ...String:
MKNPSFDWER LKDVFYRSRA IGELKWPTQY EEFKCALSLT VIAVEIQDFI QVYNYFGQLL GKINLQRIHE DIIKFEFDKD EKLILVTKS SIKIVKGWSP LTIESVPLQD PTIDTIWDYH NGIMLLAKSR DIYKLNGNEW ELLYENKDKK YNLLTKNHWS C NDDSIILL DVDHVYQVST SNGALLKLIT DSSWHKVTIS SRGFICLYNM KDNKLQIFRD PARILMEHNL DSTPDDICWC GN DTVACSF EDEIKLYGPD GLYVTFWYPF TVTNLRAEVD GLKVITTEKI YFLSRVQPQT SNIFRIGSTE PGAMLVDSFS LLE DHAPKA IEILKNFVLE KGVLDCIAAA IDEFEPKLQK MLLNAASYGK ASLQYKSFDA SIFVNACNTI KLLNCFRSFG IFLT VEEYR CISLKGVIDR LLKYHRYYEC IQICKLANER FLLGYVFTEW AKDKIKGSPD MEDDELLDKI KSRLSVIDMT DTLQM VAVA KVAYLEGRFQ LSRNLALLEK NEEARIEQLY NLDDDSIALK ECIKVQNYSL TISLLIALSK KLTNSQLTKL LIIDMF NNP LYLYYMRMDK AYLYDFYRQT DRFIDLAHVL LQQGKEQQSL HSFLPQIKDL YSQVQNSEVV NNTIEQLQRQ EKLWIYQ ES LGKRFAISFT NMTLDQTLSK LIETGQDKQV KEIVKKFKIS EKKLYHLKCK TLVEAKKFDE LLQFAQSRKS PIGYMPFY T YLKSRGHMDK ASPYVNMIPG LSYQEKKKLY VECRGFRDAI QLAGKEKDIP GLKEIYNIIP PNEPELKALA NETMSRI

UniProtKB: Vacuolar protein sorting-associated protein 16

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Macromolecule #4: E3 ubiquitin-protein ligase PEP5

MacromoleculeName: E3 ubiquitin-protein ligase PEP5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 117.617219 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLSSWRQFQ LFENIPIRDP NFGGDSLLYS DPTLCAATIV DPQTLIIAVN SNIIKVVKLN QSQVIHEFQS FPHDFQITFL KVINGEFLV ALAESIGKPS LIRVYKLEKL PNREQLYHSQ VELKNGNNTY PISVVSISND LSCIVVGFIN GKIILIRGDI S RDRGSQQR ...String:
MSLSSWRQFQ LFENIPIRDP NFGGDSLLYS DPTLCAATIV DPQTLIIAVN SNIIKVVKLN QSQVIHEFQS FPHDFQITFL KVINGEFLV ALAESIGKPS LIRVYKLEKL PNREQLYHSQ VELKNGNNTY PISVVSISND LSCIVVGFIN GKIILIRGDI S RDRGSQQR IIYEDPSKEP ITALFLNNDA TACFAATTSR ILLFNTTGRN RGRPSLVLNS KNGLDLNCGS FNPATNEFIC CL SNFIEFF SSSGKKHQFA FDLSLRKRIF CVDKDHILIV TEETGVPTTS ISVNELSPTI INRIFIIDAK NKIISLNFVV SSA IIDIFS TSQSGKNITY LLTSEGVMHR ITPKSLENQI NIIIQKELYP FALQLAKQHS LSPLDVQEIH KKYGDYLFKK GLRK EATDQ YIQCLDVVET SEIISKFGVK EVPDPESMRN LADYLWSLIK NSISQRDHVT LLLIVLIKLK DVEGIDTFIQ HFDRK GIWN EGVVMDDMDD VTFFYSDNDF FDLDLILELM KESDFKRLSY RLAKKYSKDS LIIVDILLNL LHNPVKAIKY IKSLPI DET LRCLVTYSKK LLEESPNETN ALLIEVFTGK FKPSTFEVDL DRRDTTGDFS ENIRTVFYSY KTFFNYMNSN GTSDAMS ES SEASHEHEEP TYHPPKPSIV FSSFVTKPFE FVVFLEACLA CYQQYEGFDE DRQVILTTLY DLYLNLAQND VPERIDDW R SRATGVLRES NKLVYSAASN NTSKRVDNSI MLLISHMDQS SASAKDKTKI DIASFANDNP EMDLLSTFRA MTLNEEPST CLKFLEKYGT EEPKLLQVAL SYFVSNKLIF KEMGGNEVLK EKVLRPIIEG ERMPLLDIIK ALSRTNVAHF GLIQDIIIDH VKTEDTEIK RNEKLIESYD KELKEKNKKL KNTINSDQPL HVPLKNQTCF MCRLTLDIPV VFFKCGHIYH QHCLNEEEDT L ESERKLFK CPKCLVDLET SNKLFEAQHE VVEKNDLLNF ALNSEEGSRD RFKVITEFLG RGAISYSDIT I

UniProtKB: E3 ubiquitin-protein ligase PEP5

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Macromolecule #5: Vacuolar protein sorting-associated protein 3

MacromoleculeName: Vacuolar protein sorting-associated protein 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 117.069008 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVKKKTNNDK GKEVKENEGK LDIDSESSPH ERENDKKKTE DDSLRATESE ETNTHNANPN ETVRADKFSQ EESRPIEDSP HTDKNTAQE SCQPSSAEDN VINTDITSLN EKTSTNDEQE KGLPLKISEG PFTISTLLDN VPSDLIYTCC EAYENHIFLG T TTGDLLHY ...String:
MVKKKTNNDK GKEVKENEGK LDIDSESSPH ERENDKKKTE DDSLRATESE ETNTHNANPN ETVRADKFSQ EESRPIEDSP HTDKNTAQE SCQPSSAEDN VINTDITSLN EKTSTNDEQE KGLPLKISEG PFTISTLLDN VPSDLIYTCC EAYENHIFLG T TTGDLLHY FELERGNYML VSQTKFDAES NSKIDKILLL PKVEGALILC DNELVLFILP EFAPRPNTTR LKGISDVVIC NF SRSSKAY RIYAFHAEGV RLLKISADSL VLTKAFNFKL IDKACAHEET LMVSKLNSYE LINLKSSQVI PLFRISETDE DLE PIITSF NEQSEFLVCS GGGSYDSGAM ALVVNHHGDI IKGTIVLKNY PRNVIVEFPY IIAESAFQSV DIYSALPSEK SQLL QSITT SGSDLKISKS DNVFTNTNNS EEFKEKIFNK LRLEPLTHSD NKFRIERERA FVEESYEEKT SLIVYNNLGI HLLVP TPMV LRFTSCEESE IDNIEDQLKK LAKKDLTKFE HIEAKYLMSL LLFLMTLHYD HIEDEVMKKW CDFSDKVDIR ILFYMF GWK VYSEIWCFHG LINIVERLKS LKLTNKCENI LKMLLMMKNE LKKKNKTGLL TNDFDDIMKT IDITLFKLRL EKKETIT VD MFERESYDEI IREINLHDDK LPRIELLIEI YKEKGEYLKA LNLLREAGDY ISLVSFIEEN LKKLPEDYIK ERIADDLL L TLKQGDENTE ECAIKKVLKI LDMACINKND FLNKIPAEET SLKVSFIEQL GVQNSNDSKF LFNYYLAKLR EIINQSNIW SILGDFIKEY KDDFAYDKTD ITNFIHIKLK HSLQCENFSK YYEKCENLKS ENEKDDEFIN FTFDEISKID KEHILTLLFF PNELTNWVS SEELLKIYLS FNDFRSVEKY IGKQNLVAVM KQYLDISSLN YSVELVTNLL QRNFELLDDT DIQLKILETI P SVFPVQTI SELLLKVLIK YQEKKEESNL RKCLLKNQIS ISDELSRNFD SQG

UniProtKB: Vacuolar protein sorting-associated protein 3

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Macromolecule #6: Vacuolar membrane protein PEP3

MacromoleculeName: Vacuolar membrane protein PEP3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 107.531047 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MIKTRIEEVQ LQFLTGNTEL THLKVSNDQL IVTTQRTIYR INLQDPAIVN HFDCPLSKEL ETIMNVHVSP MGSVILIRTN FGRYMLLKD GEFTQLNKIK NLDLSSLHWI NETTFLMGIK KTPKLYRVEL TGKDITTKLW YENKKLSGGI DGIAYWEGSL L LTIKDNIL ...String:
MIKTRIEEVQ LQFLTGNTEL THLKVSNDQL IVTTQRTIYR INLQDPAIVN HFDCPLSKEL ETIMNVHVSP MGSVILIRTN FGRYMLLKD GEFTQLNKIK NLDLSSLHWI NETTFLMGIK KTPKLYRVEL TGKDITTKLW YENKKLSGGI DGIAYWEGSL L LTIKDNIL YWRDVTNMKF PLVLPDESEQ FERLKHHAIK KFDSYNGLFA WVTSNGIVFG DLKEKQMEKD PASNNFGKFL SS SKVLLNF ELPDYQNDKD HLIKDIVLTA FHILLLRKNT VTMVSQLNND VVFHETIPRH QLTGSNTDSN EKFLGLVRDS VKE TFWCFS NINVFEIIIE NEPNSVWNLL VRDNKFDKAL SLKGLTVREI ESVKLSKAMY LFHTAKDFHS AAQTLGSMKD LSHF GEIAL NFLQIKDYND LNVILIKQLD NVPWKSTQVV LSSWIIWNFM KQLNDIELKI NTTKPASTDE DNLLNWNLNL KEKSN ELTK FLESHLEKLD NETVYQIMSK QNRQNELLIF ASLINDMKFL LSFWIDQGNW YESLKILLTI NNHDLVYKYS LILLLN SPE ATVSTWMKIK DLDPNKLIPT ILKFFTNWQN NSKLITNISE YPENYSLTYL KWCVREVPKM CNPIVYNSIL YMMITDP RN DMILENDIIK FMKSNENKYD LNFQLRLSLK FKKTKTSIFL LTRLNLFEDA IDLALKNNLI DDCKVIVNDE ILIEDYKL R KRLWLKIAKH LLLSMKDIDI KQLIRTILND SNEILTIKDL LPFFNEYTTI ANLKEELIKF LENHNMKMNE ISEDIINSK NLKVEINTEI SKFNEIYRIL EPGKSCDECG KFLQIKKFIV FPCGHCFHWN CIIRVILNSN DYNLRQKTEN FLKAKSKHNL NDLENIIVE KCGLCSDINI NKIDQPISID ETELAKWNE

UniProtKB: Vacuolar membrane protein PEP3

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219391
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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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

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