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- EMDB-14964: HOPS tethering complex from yeast, composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-14964
TitleHOPS tethering complex from yeast, composite map
Map dataTethering complex HOPS, composite map
Sample
  • Complex: Tethering complex HOPS
    • Protein or peptide: E3 ubiquitin-protein ligase PEP5
    • Protein or peptide: Vacuolar protein sorting-associated protein 16
    • Protein or peptide: Vacuolar membrane protein PEP3
    • Protein or peptide: Vacuolar protein sorting-associated protein 33
    • Protein or peptide: Vacuolar morphogenesis protein 6
    • Protein or peptide: Vacuolar protein sorting-associated protein 41
KeywordsHOPS / tethering complex / lysosome / membrane fusion / Rab GTPase / cryo-EM / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


histone catabolic process / organelle fusion / CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / vacuolar protein processing ...histone catabolic process / organelle fusion / CORVET complex / HOPS complex / regulation of SNARE complex assembly / endosomal vesicle fusion / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole-mitochondrion membrane contact site / vacuolar protein processing / vacuole fusion, non-autophagic / vesicle fusion with vacuole / Golgi to endosome transport / Golgi to vacuole transport / cytoplasm to vacuole targeting by the Cvt pathway / vesicle docking / endosome organization / protein targeting to vacuole / vacuole organization / late endosome to vacuole transport / fungal-type vacuole / piecemeal microautophagy of the nucleus / vesicle docking involved in exocytosis / fungal-type vacuole membrane / endosomal transport / vesicle-mediated transport / positive regulation of TORC1 signaling / cellular response to starvation / guanyl-nucleotide exchange factor activity / macroautophagy / intracellular protein transport / RING-type E3 ubiquitin transferase / autophagy / small GTPase binding / endocytosis / ubiquitin protein ligase activity / late endosome / protein transport / actin binding / protein-macromolecule adaptor activity / early endosome membrane / endosome / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 41 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 / Vacuolar sorting protein 39 domain 2 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Vacuolar sorting protein 39 domain 1 / 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-associated protein 41 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 2 / Vacuolar sorting protein 39 domain 2 / Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1 / Vacuolar protein sorting-associated protein Vps41/Vps8 / Vacuolar sorting protein 39 domain 1 / 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 protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Ring finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 membrane protein PEP3 / Vacuolar protein sorting-associated protein 41 / Vacuolar protein sorting-associated protein 16 / Vacuolar morphogenesis protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsShvarev D / Schoppe J / Koenig C / Perz A / Fuellbrunn N / Kiontke S / Langemeyer L / Januliene D / Schnelle K / Kuemmel D ...Shvarev D / Schoppe J / Koenig C / Perz A / Fuellbrunn N / Kiontke S / Langemeyer L / Januliene D / Schnelle K / Kuemmel D / Froehlich F / Moeller A / Ungermann C
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchDLR 01ED2010 Germany
CitationJournal: Elife / Year: 2022
Title: Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery.
Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian ...Authors: Dmitry Shvarev / Jannis Schoppe / Caroline König / Angela Perz / Nadia Füllbrunn / Stephan Kiontke / Lars Langemeyer / Dovile Januliene / Kilian Schnelle / Daniel Kümmel / Florian Fröhlich / Arne Moeller / Christian Ungermann /
Abstract: Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a ...Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery.
History
DepositionMay 11, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14964.png

Downloads & links

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Map

FileDownload / File: emd_14964.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTethering complex HOPS, composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 672 pix.
= 620.928 Å		0.92 Å/pix.
x 672 pix.
= 620.928 Å		0.92 Å/pix.
x 672 pix.
= 620.928 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.8176876 - 1.8933338
Average (Standard dev.)-0.00139341 (±0.0270787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 620.92804 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tethering complex HOPS

EntireName: Tethering complex HOPS
Components
  • Complex: Tethering complex HOPS
    • Protein or peptide: E3 ubiquitin-protein ligase PEP5
    • Protein or peptide: Vacuolar protein sorting-associated protein 16
    • Protein or peptide: Vacuolar membrane protein PEP3
    • Protein or peptide: Vacuolar protein sorting-associated protein 33
    • Protein or peptide: Vacuolar morphogenesis protein 6
    • Protein or peptide: Vacuolar protein sorting-associated protein 41

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Supramolecule #1: Tethering complex HOPS

SupramoleculeName: Tethering complex HOPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: E3 ubiquitin-protein ligase PEP5

MacromoleculeName: E3 ubiquitin-protein ligase PEP5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 #2: Vacuolar protein sorting-associated protein 16

MacromoleculeName: Vacuolar protein sorting-associated protein 16 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 #3: Vacuolar membrane protein PEP3

MacromoleculeName: Vacuolar membrane protein PEP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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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Macromolecule #4: Vacuolar protein sorting-associated protein 33

MacromoleculeName: Vacuolar protein sorting-associated protein 33 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 #5: Vacuolar morphogenesis protein 6

MacromoleculeName: Vacuolar morphogenesis protein 6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 123.049414 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MLRAQKLHSL KSSDITAILP TEQSQKLVLA KKNGDVEVYS RDGNTLKLFQ VYPDLLQNAK NDPLPPVIEN FYFANELSTI FAQCKETLI LLSTTNLHEY DRIIDRRGIN HCWLFERSHK NKEEKNTYLI YSTINTAKMR VLIWEGRTYK NMMEASLSYR K ETIRSIYP ...String:
MLRAQKLHSL KSSDITAILP TEQSQKLVLA KKNGDVEVYS RDGNTLKLFQ VYPDLLQNAK NDPLPPVIEN FYFANELSTI FAQCKETLI LLSTTNLHEY DRIIDRRGIN HCWLFERSHK NKEEKNTYLI YSTINTAKMR VLIWEGRTYK NMMEASLSYR K ETIRSIYP GETGITLATD LGIYHWPYNK PSLIRIEKTV KNKFPKDMIS ALTELKEQAE KVIEKKPKKN SHFDAQSFSS MD RMSRKSS MSSLWYRTIR NERGNKIRYT FELDGNDATP MIIDGATKKI FKVELMHNNE EPFLIATDHA TFSESNSEFD HMQ YLSSNL LMLYNSSTIK FVDYENGFTF LQQKIPEGIK WVKNLSGTYF LVWTSNDEVQ LFSYHVDDGS EDDDQESICG DIND PDFYQ LWRKVLFYKF FIDSPHSKEL CVSDNPEESL DICAMKLRDL TVMWCLRIFD KFQNYMVQLE RSRNSRMIRS KCEEM IIKS IFDLFIKFWA PPQLVILKVF PSAISSLVLE ITGQEHHCLL KEAEEVKETY DIPPHLLNRW CLPYLTDTRR HLQNLL SKE NDDESRITWC YRDREIKQSF DFFLISNHDD VDLNTMLTLI DTVLFKCYLY YNPPMVGPFI RVENHCDSHV IVTELKI RH MFKDLIDFYY KRGNHEEALK FLTDLVDELE NDNTDQKQRQ KIDHGVKILV IYYLKKLSNP QLDVIFTYTD WLLNRHND S IKEILSSIFF YDSQACSSRD HLKVYGYIKK FDKLLAIQYL EFAISTFRLE GNKLHTVLIK LYLENLDIPS TRIKLKSLL ETTSVYEPRT ILKLLNDAIE SGSDQLPTNQ LNFVKYLKIF PLSKLENHKE AVHILLDEID DYKAATSYCN DVYQSDSTKG EELLLYLYS KLVSIYDSNR NSKLILNFLQ DHGSKLNSAE IYKNLPQDIS LYDIGRVVSQ LLKKHTSKMD ETRLEKALLQ V ELVATTYK LNERMSSYGV LSDSHKCPIC KKVISNFGTD SISWFTREGR NIITHYNCGK VLQERFNAKN EKSSRIKQKT LG EVINELN NK

UniProtKB: Vacuolar morphogenesis protein 6

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Macromolecule #6: Vacuolar protein sorting-associated protein 41

MacromoleculeName: Vacuolar protein sorting-associated protein 41 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 116.530555 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS CISQAENGVA SRTDESTITG SATDAETGDD DDDDDDDDD EDEDDEDEPP LLKYTRISQL PKNFFQRDSI SSCLFGDTFF AFGTHSGILH LTTCAFEPIK TIKCHRSSIL C INTDGKYF ...String:
MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS CISQAENGVA SRTDESTITG SATDAETGDD DDDDDDDDD EDEDDEDEPP LLKYTRISQL PKNFFQRDSI SSCLFGDTFF AFGTHSGILH LTTCAFEPIK TIKCHRSSIL C INTDGKYF ATGSIDGTVI IGSMDDPQNI TQYDFKRPIN SVALHSNFQA SRMFVSGGMA GDVVLSQRNW LGNRIDIVLN KK KKKKTRK DDLSSDMKGP IMGIYTMGDL ILWMDDDGIT FCDVPTRSQL LNIPFPSRIF NVQDVRPDLF RPHVHFLESD RVV IGWGSN IWLFKVSFTK DSNSIKSGDS NSQSNNMSHF NPTTNIGSLL SSAASSFRGT PDKKVELECH FTVSMLITGL ASFK DDQLL CLGFDIDIEE EATIDEDMKE GKNFSKRPEN LLAKGNAPEL KIVDLFNGDE IYNDEVIMKN YEKLSINDYH LGKHI DKTT PEYYLISSND AIRVQELSLK DHFDWFMERK QYYKAWKIGK YVIGSEERFS IGLKFLNSLV TKKDWGTLVD HLNIIF EET LNSLDSNSYD VTQNVLKEWA DIIEILITSG NIVEIAPLIP KKPALRKSVY DDVLHYFLAN DMINKFHEYI TKWDLKL FS VEDFEEELET RIEAASEPTA SSKEEGSNIT YRTELVHLYL KENKYTKAIP HLLKAKDLRA LTIIKIQNLL PQYLDQIV D IILLPYKGEI SHISKLSIFE IQTIFNKPID LLFENRHTIS VARIYEIFEH DCPKSFKKIL FCYLIKFLDT DDSFMISPY ENQLIELYSE YDRQSLLPFL QKHNNYNVES AIEVCSSKLG LYNELIYLWG KIGETKKALS LIIDELKNPQ LAIDFVKNWG DSELWEFMI NYSLDKPNFT KAILTCSDET SEIYLKVIRG MSDDLQIDNL QDIIKHIVQE NSLSLEVRDN ILVIINDETK K FANEFLKI RSQGKLFQVD ESDIEINDDL NGVLDYKDDD DKDYKDDDDK DYKDDDDK

UniProtKB: Vacuolar protein sorting-associated protein 41

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K / 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: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: OTHER
Details: Resolution of the consensus map of the lower part of the complex is used here
Number images used: 244661
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)

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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

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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

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