HOPS tethering complex from yeast, composite map

2025-04-16 REL PDBe INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY entity entity_name_com entity_src_gen struct_ref struct_ref_seq _entity.pdbx_description _entity_src_gen.gene_src_strain _entity_src_gen.pdbx_gene_src_gene _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref_seq.pdbx_db_accession DATABASE_REFERENCES pdbx_database_related DATABASE_REFERENCES chem_comp_atom chem_comp_bond citation citation_author em_admin _em_admin.last_update STRUCTURE_SUMMARY citation citation_author em_admin pdbx_entry_details _em_admin.last_update PDBe PDBe 2022-05-11 2022-09-28 2022-09-28 2025-04-16 German Research Foundation (DFG) SFB 944 Germany German Research Foundation (DFG) INST190/196-1 FUGG Germany German Federal Ministry for Education and Research DLR 01ED2010 Germany HOPS tethering complex from yeast, composite map 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 HOPS, tethering complex, lysosome, membrane fusion, Rab GTPase, cryo-EM, CYTOSOLIC PROTEIN Shvarev D Schoppe J Konig C Perz A Fullbrunn N Kiontke S Langemeyer L Januliene D Schnelle K Kummel D Frohlich F Moeller A Ungermann C Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery. Elife US 11 2022 36098503 doi:10.7554/eLife.80901 2050-084X Shvarev D Konig C Susan N Langemeyer L Walter S Perz A Frohlich F Ungermann C Moeller A Structure of the endosomal CORVET tethering complex. Nat Commun UK 15 5227 5227 2024 38898033 doi:10.1038/s41467-024-49137-9 2041-1723 Shvarev D Schoppe J Konig C Perz A Fullbrunn N Kiontke S Langemeyer L Januliene D Schnelle K Kummel D Frohlich F Moeller A Ungermann C Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery. Elife US 11 2022 36098503 doi:10.7554/eLife.80901 2050-084X EMD-14965 other EM volume

consensus map covering the upper part of the complex

EMD-14966 other EM volume

consensus map covering the bottom part of the complex

EMD-14967 other EM volume

local refinement map of the SNARE-binding module (based on EMD-14965 consensus map)

EMD-14968 other EM volume

local refinement map of the backbone part of the complex (based on EMD-14965 consensus map)

EMD-14969 other EM volume

local refinement map of the bottom part of the complex (Vps18) (based on EMD-14966 consensus map)

EMD-14970 other EM volume

local refinement map of the bottom part of the complex (Vps39) (based on EMD-14966 consensus map)

7zu0 FULLOVERLAP Tethering complex HOPS Tethering complex HOPS 0 1 2 3 4 5 6 Saccharomyces cerevisiae E3 ubiquitin-protein ligase PEP5 Saccharomyces cerevisiae ATCC 204508 / S288c 0.117617219 1 Saccharomyces cerevisiae LEVO MSLSSWRQFQLFENIPIRDPNFGGDSLLYSDPTLCAATIVDPQTLIIAVNSNIIKVVKLNQSQVIHEFQSFPHDFQITFL KVINGEFLVALAESIGKPSLIRVYKLEKLPNREQLYHSQVELKNGNNTYPISVVSISNDLSCIVVGFINGKIILIRGDIS RDRGSQQRIIYEDPSKEPITALFLNNDATACFAATTSRILLFNTTGRNRGRPSLVLNSKNGLDLNCGSFNPATNEFICCL SNFIEFFSSSGKKHQFAFDLSLRKRIFCVDKDHILIVTEETGVPTTSISVNELSPTIINRIFIIDAKNKIISLNFVVSSA IIDIFSTSQSGKNITYLLTSEGVMHRITPKSLENQINIIIQKELYPFALQLAKQHSLSPLDVQEIHKKYGDYLFKKGLRK EATDQYIQCLDVVETSEIISKFGVKEVPDPESMRNLADYLWSLIKNSISQRDHVTLLLIVLIKLKDVEGIDTFIQHFDRK GIWNEGVVMDDMDDVTFFYSDNDFFDLDLILELMKESDFKRLSYRLAKKYSKDSLIIVDILLNLLHNPVKAIKYIKSLPI DETLRCLVTYSKKLLEESPNETNALLIEVFTGKFKPSTFEVDLDRRDTTGDFSENIRTVFYSYKTFFNYMNSNGTSDAMS ESSEASHEHEEPTYHPPKPSIVFSSFVTKPFEFVVFLEACLACYQQYEGFDEDRQVILTTLYDLYLNLAQNDVPERIDDW RSRATGVLRESNKLVYSAASNNTSKRVDNSIMLLISHMDQSSASAKDKTKIDIASFANDNPEMDLLSTFRAMTLNEEPST CLKFLEKYGTEEPKLLQVALSYFVSNKLIFKEMGGNEVLKEKVLRPIIEGERMPLLDIIKALSRTNVAHFGLIQDIIIDH VKTEDTEIKRNEKLIESYDKELKEKNKKLKNTINSDQPLHVPLKNQTCFMCRLTLDIPVVFFKCGHIYHQHCLNEEEDTL ESERKLFKCPKCLVDLETSNKLFEAQHEVVEKNDLLNFALNSEEGSRDRFKVITEFLGRGAISYSDITI P12868 2.3.2.27 Vacuolar protein sorting-associated protein 16 Saccharomyces cerevisiae ATCC 204508 / S288c 0.092857 1 Saccharomyces cerevisiae LEVO MKNPSFDWERLKDVFYRSRAIGELKWPTQYEEFKCALSLTVIAVEIQDFIQVYNYFGQLLGKINLQRIHEDIIKFEFDKD EKLILVTKSSIKIVKGWSPLTIESVPLQDPTIDTIWDYHNGIMLLAKSRDIYKLNGNEWELLYENKDKKYNLLTKNHWSC NDDSIILLDVDHVYQVSTSNGALLKLITDSSWHKVTISSRGFICLYNMKDNKLQIFRDPARILMEHNLDSTPDDICWCGN DTVACSFEDEIKLYGPDGLYVTFWYPFTVTNLRAEVDGLKVITTEKIYFLSRVQPQTSNIFRIGSTEPGAMLVDSFSLLE DHAPKAIEILKNFVLEKGVLDCIAAAIDEFEPKLQKMLLNAASYGKASLQYKSFDASIFVNACNTIKLLNCFRSFGIFLT VEEYRCISLKGVIDRLLKYHRYYECIQICKLANERFLLGYVFTEWAKDKIKGSPDMEDDELLDKIKSRLSVIDMTDTLQM VAVAKVAYLEGRFQLSRNLALLEKNEEARIEQLYNLDDDSIALKECIKVQNYSLTISLLIALSKKLTNSQLTKLLIIDMF NNPLYLYYMRMDKAYLYDFYRQTDRFIDLAHVLLQQGKEQQSLHSFLPQIKDLYSQVQNSEVVNNTIEQLQRQEKLWIYQ ESLGKRFAISFTNMTLDQTLSKLIETGQDKQVKEIVKKFKISEKKLYHLKCKTLVEAKKFDELLQFAQSRKSPIGYMPFY TYLKSRGHMDKASPYVNMIPGLSYQEKKKLYVECRGFRDAIQLAGKEKDIPGLKEIYNIIPPNEPELKALANETMSRI Q03308 Vacuolar membrane protein PEP3 Saccharomyces cerevisiae ATCC 204508 / S288c 0.107531047 1 Saccharomyces cerevisiae LEVO MIKTRIEEVQLQFLTGNTELTHLKVSNDQLIVTTQRTIYRINLQDPAIVNHFDCPLSKELETIMNVHVSPMGSVILIRTN FGRYMLLKDGEFTQLNKIKNLDLSSLHWINETTFLMGIKKTPKLYRVELTGKDITTKLWYENKKLSGGIDGIAYWEGSLL LTIKDNILYWRDVTNMKFPLVLPDESEQFERLKHHAIKKFDSYNGLFAWVTSNGIVFGDLKEKQMEKDPASNNFGKFLSS SKVLLNFELPDYQNDKDHLIKDIVLTAFHILLLRKNTVTMVSQLNNDVVFHETIPRHQLTGSNTDSNEKFLGLVRDSVKE TFWCFSNINVFEIIIENEPNSVWNLLVRDNKFDKALSLKGLTVREIESVKLSKAMYLFHTAKDFHSAAQTLGSMKDLSHF GEIALNFLQIKDYNDLNVILIKQLDNVPWKSTQVVLSSWIIWNFMKQLNDIELKINTTKPASTDEDNLLNWNLNLKEKSN ELTKFLESHLEKLDNETVYQIMSKQNRQNELLIFASLINDMKFLLSFWIDQGNWYESLKILLTINNHDLVYKYSLILLLN SPEATVSTWMKIKDLDPNKLIPTILKFFTNWQNNSKLITNISEYPENYSLTYLKWCVREVPKMCNPIVYNSILYMMITDP RNDMILENDIIKFMKSNENKYDLNFQLRLSLKFKKTKTSIFLLTRLNLFEDAIDLALKNNLIDDCKVIVNDEILIEDYKL RKRLWLKIAKHLLLSMKDIDIKQLIRTILNDSNEILTIKDLLPFFNEYTTIANLKEELIKFLENHNMKMNEISEDIINSK NLKVEINTEISKFNEIYRILEPGKSCDECGKFLQIKKFIVFPCGHCFHWNCIIRVILNSNDYNLRQKTENFLKAKSKHNL NDLENIIVEKCGLCSDININKIDQPISIDETELAKWNE P27801 Vacuolar protein sorting-associated protein 33 Saccharomyces cerevisiae ATCC 204508 / S288c 0.079354977 1 Saccharomyces cerevisiae LEVO MNRFWNTKKFSLTNADGLCATLNEISQNDEVLVVQPSVLPVLNSLLTFQDLTQSTPVRKITLLDDQLSDDLPSALGSVPQ MDLIFLIDVRTSLRLPPQLLDAAQKHNLSSLHIIYCRWKPSFQNTLEDTEQWQKDGFDLNSKKTHFPNVIESQLKELSNE YTLYPWDLLPFPQIDENVLLTHSLYNMENVNMYYPNLRSLQSATESILVDDMVNSLQSLIFETNSIITNVVSIGNLSKRC SHLLKKRIDEHQTENDLFIKGTLYGERTNCGLEMDLIILERNTDPITPLLTQLTYAGILDDLYEFNSGIKIKEKDMNFNY KEDKIWNDLKFLNFGSIGPQLNKLAKELQTQYDTRHKAESVHEIKEFVDSLGSLQQRQAFLKNHTTLSSDVLKVVETEEY GSFNKILELELEILMGNTLNNDIEDIILELQYQYEVDQKKILRLICLLSLCKNSLREKDYEYLRTFMIDSWGIEKCFQLE SLAELGFFTSKTGKTDLHITTSKSTRLQKEYRYISQWFNTVPIEDEHAADKITNENDDFSEATFAYSGVVPLTMRLVQML YDRSILFHNYSSQQPFILSREPRVSQTEDLIEQLYGDSHAIEESIWVPGTITKKINASIKSNNRRSIDGSNGTFHAAEDI ALVVFLGGVTMGEIAIMKHLQKILGKKGINKRFIIIADGLINGTRIMNSIS P20795 Vacuolar morphogenesis protein 6 Saccharomyces cerevisiae ATCC 204508 / S288c 0.123049414 1 Saccharomyces cerevisiae LEVO MLRAQKLHSLKSSDITAILPTEQSQKLVLAKKNGDVEVYSRDGNTLKLFQVYPDLLQNAKNDPLPPVIENFYFANELSTI FAQCKETLILLSTTNLHEYDRIIDRRGINHCWLFERSHKNKEEKNTYLIYSTINTAKMRVLIWEGRTYKNMMEASLSYRK ETIRSIYPGETGITLATDLGIYHWPYNKPSLIRIEKTVKNKFPKDMISALTELKEQAEKVIEKKPKKNSHFDAQSFSSMD RMSRKSSMSSLWYRTIRNERGNKIRYTFELDGNDATPMIIDGATKKIFKVELMHNNEEPFLIATDHATFSESNSEFDHMQ YLSSNLLMLYNSSTIKFVDYENGFTFLQQKIPEGIKWVKNLSGTYFLVWTSNDEVQLFSYHVDDGSEDDDQESICGDIND PDFYQLWRKVLFYKFFIDSPHSKELCVSDNPEESLDICAMKLRDLTVMWCLRIFDKFQNYMVQLERSRNSRMIRSKCEEM IIKSIFDLFIKFWAPPQLVILKVFPSAISSLVLEITGQEHHCLLKEAEEVKETYDIPPHLLNRWCLPYLTDTRRHLQNLL SKENDDESRITWCYRDREIKQSFDFFLISNHDDVDLNTMLTLIDTVLFKCYLYYNPPMVGPFIRVENHCDSHVIVTELKI RHMFKDLIDFYYKRGNHEEALKFLTDLVDELENDNTDQKQRQKIDHGVKILVIYYLKKLSNPQLDVIFTYTDWLLNRHND SIKEILSSIFFYDSQACSSRDHLKVYGYIKKFDKLLAIQYLEFAISTFRLEGNKLHTVLIKLYLENLDIPSTRIKLKSLL ETTSVYEPRTILKLLNDAIESGSDQLPTNQLNFVKYLKIFPLSKLENHKEAVHILLDEIDDYKAATSYCNDVYQSDSTKG EELLLYLYSKLVSIYDSNRNSKLILNFLQDHGSKLNSAEIYKNLPQDISLYDIGRVVSQLLKKHTSKMDETRLEKALLQV ELVATTYKLNERMSSYGVLSDSHKCPICKKVISNFGTDSISWFTREGRNIITHYNCGKVLQERFNAKNEKSSRIKQKTLG EVINELNNK Q07468 Vacuolar protein sorting-associated protein 41 Saccharomyces cerevisiae ATCC 204508 / S288c 0.116530555 1 Saccharomyces cerevisiae LEVO MTTDNHQNDSVLDQQSGERTIDESNSISDENNVDNKREDVNVTSPTKSVSCISQAENGVASRTDESTITGSATDAETGDD DDDDDDDDDEDEDDEDEPPLLKYTRISQLPKNFFQRDSISSCLFGDTFFAFGTHSGILHLTTCAFEPIKTIKCHRSSILC INTDGKYFATGSIDGTVIIGSMDDPQNITQYDFKRPINSVALHSNFQASRMFVSGGMAGDVVLSQRNWLGNRIDIVLNKK KKKKTRKDDLSSDMKGPIMGIYTMGDLILWMDDDGITFCDVPTRSQLLNIPFPSRIFNVQDVRPDLFRPHVHFLESDRVV IGWGSNIWLFKVSFTKDSNSIKSGDSNSQSNNMSHFNPTTNIGSLLSSAASSFRGTPDKKVELECHFTVSMLITGLASFK DDQLLCLGFDIDIEEEATIDEDMKEGKNFSKRPENLLAKGNAPELKIVDLFNGDEIYNDEVIMKNYEKLSINDYHLGKHI DKTTPEYYLISSNDAIRVQELSLKDHFDWFMERKQYYKAWKIGKYVIGSEERFSIGLKFLNSLVTKKDWGTLVDHLNIIF EETLNSLDSNSYDVTQNVLKEWADIIEILITSGNIVEIAPLIPKKPALRKSVYDDVLHYFLANDMINKFHEYITKWDLKL FSVEDFEEELETRIEAASEPTASSKEEGSNITYRTELVHLYLKENKYTKAIPHLLKAKDLRALTIIKIQNLLPQYLDQIV DIILLPYKGEISHISKLSIFEIQTIFNKPIDLLFENRHTISVARIYEIFEHDCPKSFKKILFCYLIKFLDTDDSFMISPY ENQLIELYSEYDRQSLLPFLQKHNNYNVESAIEVCSSKLGLYNELIYLWGKIGETKKALSLIIDELKNPQLAIDFVKNWG DSELWEFMINYSLDKPNFTKAILTCSDETSEIYLKVIRGMSDDLQIDNLQDIIKHIVQENSLSLEVRDNILVIINDETKK FANEFLKIRSQGKLFQVDESDIEINDDLNGVLDYKDDDDKDYKDDDDKDYKDDDDK P38959 singleParticle particle 7.4 ETHANE 100 277 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.8 2.8000000000000003 FEI FALCON IV (4k x 4k) 50.0 1 4.4 OTHER

Resolution of the consensus map of the lower part of the complex is used here

244661 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 emd_14964.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 672 672 672 0 0 0 672 672 672 620.92804 620.92804 620.92804 90.0 90.0 90.0 X Y Z -0.8176876 1.8933338 -0.00139341 0.0270787 0.9240001 0.9240001 0.9240001 0.35 AUTHOR ::::EMDATABANK.org::::EMD-14964:::: Tethering complex HOPS, composite map