2024-08-07 REL RCSB RCSB RCSB 2024-05-11 2024-06-19 2024-06-19 2024-08-07 Howard Hughes Medical Institute (HHMI) United States National Institutes of Health/National Institute of Mental Health (NIH/NIMH) RO1MH63105 United States Wang C Jiang W Yang K Wang X Guo Q Brunger AT V-ATPase, synaptic vesicle, MEMBRANE PROTEIN Wang C Jiang W Leitz J Yang K Esquivies L Wang X Shen X Held RG Adams DJ Basta T Hampton L Jian R Jiang L Stowell MHB Baumeister W Guo Q Brunger AT Nature UK 631 899 904 2024 38838737 doi:10.1038/s41586-024-07610-x 1476-4687 0006 NATUAS 9brs FULLOVERLAP Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Mus musculus V-type proton ATPase subunit E 1 Mus musculus 0.026196449

VATE1_MOUSE V-type proton ATPase subunit E 1

3 LEVO MALSDADVQKQIKHMMAFIEQEANEKAEEIDAKAEEEFNIEKGRLVQTQRLKIMEYYEKKEKQIEQQKKIQMSNLMNQAR LKVLRARDDLITDLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIVRCRKQDFPLVKAAVQKAIPMYKIATK KDVDVQIDQEAYLPEEIAGGVEIYNGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD P50518 V-type proton ATPase subunit G 2 Mus musculus 0.013674476

VATG2_MOUSE V-type proton ATPase subunit G 2

3 LEVO MASQTQGIQQLLQAEKRAAEKVADARKRKARRLKQAKEEAQMEVEQYRREREQEFQSKQQAAMGSQGNLSAEVEQATRRQ VQGMQSSQQRNRERVLAQLLGMVCEVRPQVHPNYRVTV Q9WTT4 V-type proton ATPase subunit C 1 Mus musculus 0.043945449

VATC1_MOUSE V-type proton ATPase subunit C 1

1 LEVO MTEFWLISAPGEKTCQQTWEKLHAATTKNNNLAVSSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVL EDSKDKVQENLLASGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVTQIDNDLKSRASAYNNLKGNLQNLERKNAGS LLTRSLAEIVKKDDFVLDSEYLVTLLVVVPKLNHNDWIKQYETLAEMVVPRSSNVLSEDQDSYLCNVTLFRKAVDDFRHK ARENKFIVRDFQYNEEEMKADKEEMTRLSTDKKKQFGPLVRWLKVNFSEAFIAWIHIKALRVFVESVLRYGLPVNFQAML LQPNKKSVKKLREVLHELYKHLDSSAAAIIDAPMDIPGLNLSQQEYYPYVYYKIDCNLLEFK Q9Z1G3 V-type proton ATPase subunit H Mus musculus 0.05592285899999999

VATH_MOUSE V-type proton ATPase subunit H

1 LEVO MTKMDIRGAVDAAVPTNIIAAKAAEVRANKVNWQSYLQGQMISAEDCEFIQRFEMKRSSEDKQEMLQTEGSQCAKTFINL MTHISKEQTVQYILTMVDDMLQENHQRVSIFFDYAKRSKSTAWPYFLPMLNRQDPFTVHMAARIIAKLAAWGKELMEGSD LNYYFNWIKTQLSSQKLRGSGVAVETGTISSSDSSQYVQCVAGCLQLMLRVNEYRFAWVEADGVNCIMGVLSNKCGFQLQ YQMIFSIWLLAFSPQMCEHLRRYNIIPVLSDILQESVKEKVTRIILAAFRNFLEKSTERETRQEYALAMIQCKVLKQLEN LEQQKYDDEDISEDIKFLLEKLGESVQDLSSFDEYSSELKSGRLEWSPVHKSEKFWRENAVRLNEKNYELLKILTKLLEV SDDPQVLAVAAHDVGEYVRHYPRGKRVIEQLGGKQLVMNHMHHEDQQVRYNALLAVQKLMVHNWEYLGKQLQSEQPQTAA ARS Q8BVE3 V-type proton ATPase 116 kDa subunit a 1 Mus musculus 0.0964425

VPP1_MOUSE V-type proton ATPase 116 kDa subunit a isoform 1

1 LEVO MGELFRSEEMTLAQLFLQSEAAYCCVSELGELGKVQFRDLNPDVNVFQRKFVNEVRRCEEMDRKLRFVEKEIRKANIPIM DTGENPEVPFPRDMIDLEANFEKIENELKEINTNQEALKRNFLELTELKFILRKTQQFFDEAELHHQQMADPDLLEESSS LLEPNEMGRGAPLRLGFVAGVINRERIPTFERMLWRVCRGNVFLRQAEIENPLEDPVTGDYVHKSVFIIFFQGDQLKNRV KKICEGFRASLYPCPETPQERKEMASGVNTRIDDLQMVLNQTEDHRQRVLQAAAKNIRVWFIKVRKMKAIYHTLNLCNID VTQKCLIAEVWCPVTDLDSIQFALRRGTEHSGSTVPSILNRMQTNQTPPTYNKTNKFTHGFQNIVDAYGIGTYREINPAP YTVITFPFLFAVMFGDFGHGILMTLFAVWMVLRESRILSQKHENEMFSMVFSGRYIILLMGLFSIYTGLIYNDCFSKSLN IFGSSWSVRPMFTQGNWTEETLLGSSVLQLNPAIPGVFGGPYPFGIDPIWNIATNKLTFLNSFKMKMSVILGIIHMLFGV SLSLFNHIYFKKPLNIYFGFIPEIIFMSSLFGYLVILIFYKWTAYDAHSSRNAPSLLIHFINMFLFSYPESGNAMLYSGQ KGIQCFLIVVAMLCVPWMLLFKPLILRHQYLRKKHLGTLNFGGIRVGNGPTEEDAEIIQHDQLSTHSEDAEEFDFGDTMV HQAIHTIEYCLGCISNTASYLRLWALSLAHAQLSEVLWTMVIHIGLHVRSLAGGLGLFFIFAAFATLTVAILLIMEGLSA FLHALRLHWVEFQNKFYTGTGFKFLPFSFEHIREGKFD Q9Z1G4 V-type proton ATPase subunit e 2 Mus musculus 0.00920302

VA0E2_MOUSE V-type proton ATPase subunit e 2

1 LEVO MTAHSFALPVIIFTTFWGLIGIAGPWFVPKGPNRGVIITMLVATAVCCYLFWLIAILAQLNPLFGPQLKNETIWYVRFLW E Q91XE7 Ribonuclease kappa Mus musculus 0.011000004

RNK_MOUSE Ribonuclease kappa

1 LEVO MASLLCCGPKLAACGIVLSAWGVIMLIMLGIFFNVHSAVLIEDVPFTEKDFENGPQNIYNLYEQVSYNCFIAAGLYLLLG GFSFCQVRLNKRKEYMVR Q8K3C0 3.1.-.- V-type proton ATPase subunit F Mus musculus 0.013389262

VATF_MOUSE V-type proton ATPase subunit F

1 LEVO MAGRGKLIAVIGDEDTVTGFLLGGIGELNKNRHPNFLVVEKDTTINEIEDTFRQFLNRDDIGIILINQYIAEMVRHALDA HQRSIPAVLEIPSKEHPYDAAKDSILRRAKGMFTAEDLR Q9D1K2 V-type proton ATPase subunit d 1 Mus musculus 0.040341933999999996

VA0D1_MOUSE V-type proton ATPase subunit d 1

1 LEVO MSFFPELYFNVDNGYLEGLVRGLKAGVLSQADYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVIDDKLKEKMVV EFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEAVNIAQTPAELYNAILVDTPL AAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCPILEFEADRRAFIITINSFGTELSKEDRAKL FPHCGRLYPEGLAQLARADDYEQVKNVADYYPEYKLLFEGAGSNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVK LKEQECRNIVWIAECIAQRHRAKIDNYIPIF P51863 V-type proton ATPase subunit S1 Mus musculus 0.05104621499999999

VAS1_MOUSE V-type proton ATPase subunit S1

1 LEVO MMAATVVSRIRTGTGRAPVMWLSLSLVAVAAAVATEQQVPLVLWSSDRNLWAPVADTHEGHITSDMQLSTYLDPALELGP RNVLLFLQDKLSIEDFTAYGGVFGNKQDSAFSNLENALDLAPSSLVLPAVDWYAISTLTTYLQEKLGASPLHVDLATLKE LKLNASLPALLLIRLPYTASSGLMAPREVLTGNDEVIGQVLSTLKSEDVPYTAALTAVRPSRVARDITMVAGGLGRQLLQ TQVASPAIHPPVSYNDTAPRILFWAQNFSVAYKDEWKDLTSLTFGVENLNLTGSFWNDSFAMLSLTYEPLFGATVTFKFI LASRFYPVSARYWFAMERLEIHSNGSVAHFNVSQVTGPSIYSFHCEYVSSVSKKGNLLVTNVPSVWQMTLHNFQIQAFNV TGEQFSYASDCAGFFSPGIWMGLLTTLFMLFIFTYGLHMILSLKTMDRFDDHKGPTITLTQIV Q9R1Q9 Renin receptor cytoplasmic fragment Mus musculus 0.039128789

RENR_MOUSE Renin receptor

1 LEVO MAVLVVLLFFLVAGALGNEFSILRSPGSVVFRNGNWPIPGDRIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATIMVM VKGVDKLALPAGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTLRQLRNRLF QENSLLNSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDELGKRYGEDSEQFRDASKI LVDALQKFADDMYSLYGGNAVVELVTVKSFDTSLVRKSRTILEAKQENTQSPYNLAYKYNLEYSVVFNLVLWIMIGLALA VIITSYNIWNMDPGYDSIIYRMTNQKIRID Q9CYN9 V-type proton ATPase 21 kDa proteolipid subunit c'' Mus musculus 0.021618553

VATO_MOUSE V-type proton ATPase 21 kDa proteolipid subunit

1 LEVO MTGLELLYLGIFVAFWACMVVVGICYTIFDLGFRFDVAWFLTETSPFMWSNLGIGLAISLSVVGAAWGIYITGSSIIGGG VKAPRIKTKNLVSIIFCEAVAIYGIIMAIVISNMAEPFSATEPKAIGHRNYHAGYSMFGAGLTVGLSNLFCGVCVGIVGS GAALADAQNPSLFVKILIVEIFGSAIGLFGVIVAILQTSRVKMGD Q91V37 V-type proton ATPase 16 kDa proteolipid subunit c Mus musculus 0.015815833

VATL_MOUSE V-type proton ATPase 16 kDa proteolipid subunit

9 LEVO MADIKNNPEYSSFFGVMGASSAMVFSAMGAAYGTAKSGTGIAAMSVMRPELIMKSIIPVVMAGIIAIYGLVVAVLIANSL TDGITLYRSFLQLGAGLSVGLSGLAAGFAIGIVGDAGVRGTAQQPRLFVGMILILIFAEVLGLYGLIVALILSTK P63082 V-type proton ATPase catalytic subunit A Mus musculus 0.068402875

VATA_MOUSE V-type proton ATPase catalytic subunit A

3 LEVO MDFSKLPKIRDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVL RTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDIKWEFIPSKNLRVGSHITGGDIYGIVNENS LIKHKIMLPPRNRGSVTYIAPPGNYDASDVVLELEFEGVKEKFSMVQVWPVRQVRPVTEKLPANHPLLTGQRVLDALFPC VQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGERGNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPV AAREASIYTGITLSEYFRDMGYHVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPER EGSVSIVGAVSPPGGDFSDPVTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAK EILQEEEDLAEIVQLVGKASLAETDKITLEVAKLIKDDFLQQNGYTPYDRFCPFYKTVGMLSNMISFYDMARRAVETTAQ SDNKITWSIIREHMGEILYKLSSMKFKDPVKDGEAKIKADYAQLLEDMQNAFRSLED P50516 7.1.2.2 V-type proton ATPase subunit B, brain isoform Mus musculus 0.05661157

VATB2_MOUSE V-type proton ATPase subunit B

3 LEVO MALRAMRGIVNGAAPELPVPTGGPMAGAREQALAVSRNYLSQPRLTYKTVSGVNGPLVILDHVKFPRYAEIVHLTLPDGT KRSGQVLEVSGSKAVVQVFEGTSGIDAKKTSCEFTGDILRTPVSEDMLGRVFNGSGKPIDRGPVVLAEDFLDIMGQPINP QCRIYPEEMIQTGISAIDGMNSIARGQKIPIFSAAGLPHNEIAAQICRQAGLVKKSKDVVDYSEENFAIVFAAMGVNMET ARFFKSDFEENGSMDNVCLFLNLANDPTIERIITPRLALTTAEFLAYQCEKHVLVILTDMSSYAEALREVSAAREEVPGR RGFPGYMYTDLATIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQLHNRQIYPPINVLPSLSR LMKSAIGEGMTRKDHADVSNQLYACYAIGKDVQAMKAVVGEEALTSDDLLYLEFLQKFEKNFITQGPYENRTVYETLDIG WQLLRIFPKEMLKRIPQSTLSEFYPRDSAKH P62814 V-type proton ATPase subunit D Mus musculus 0.028419116999999997

VATD_MOUSE V-type proton ATPase subunit D

1 LEVO MSGKDRIEIFPSRMAQTIMKARLKGAQTGRNLLKKKSDALTLRFRQILKKIIETKMLMGEVMREAAFSLAEAKFTAGDFS TTVIQNVNKAQVKIRAKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQLAKLKRNYAKAVELLVELASLQTSFVTLDE AIKITNRRVNAIEHVIIPRIERTLAYIITELDEREREEFYRLKKIQEKKKIIKEKFEKDLERRRAAGEVMEPANLLAEEK DEDLLFE P57746 singleParticle cell 7.4 ETHANE

The specimen state should be an intact subcellular component.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 50.0 1 4.4 FSC 0.143 CUT-OFF 30487 RANDOM ASSIGNMENT MAXIMUM LIKELIHOOD FLEXIBLE FIT emd_44842_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 495.48798 495.48798 495.48798 90.0 90.0 90.0 X Y Z -0.0016536295 2.0802817 0.0027891232 0.038745534 1.106 1.106 1.106 AUTHOR ::::EMDATABANK.org::::EMD-44842:::: EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs. emd_44842_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 495.6672 495.6672 495.6672 90.0 90.0 90.0 X Y Z -0.010071899 0.014378387 0.0000019153044 0.00048480707 1.1064 1.1064 1.1064 AUTHOR ::::EMDATABANK.org::::EMD-44842:::: Unsharpened map emd_44842_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 495.6672 495.6672 495.6672 90.0 90.0 90.0 X Y Z -0.024664804 0.028918136 0.0000018043023 0.002046635 1.1064 1.1064 1.1064 AUTHOR ::::EMDATABANK.org::::EMD-44842:::: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs. emd_44842_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 495.6672 495.6672 495.6672 90.0 90.0 90.0 X Y Z -0.02546157 0.028384965 0.0000019889135 0.002068224 1.1064 1.1064 1.1064 AUTHOR ::::EMDATABANK.org::::EMD-44842:::: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.