2025-09-03 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update RCSB RCSB 2024-12-11 2025-02-12 2025-02-12 2025-09-03 Aligning Science Across Parkinsons (ASAP) ASAP-000350 United States Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Cook ASI Hurley JH Chen M Complex, GTPase, GTP-binding, Autophagy, Kinase, Lipid Kinase, SIGNALING PROTEIN Cook ASI Chen M Nguyen TN Cabezudo AC Khuu G Rao S Garcia SN Yang M Iavarone AT Ren X Lazarou M Hummer G Hurley JH Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Science US 388 eadl3787 eadl3787 2025 39913640 doi:10.1126/science.adl3787 1095-9203 0038 SCIEAS EMD-48257 consensus EM volume
Consensus refinement of 160k particle stack
 EMD-48258 focused EM volume
Local refinment of the VPS34/VPS15 kinase/pseudokinase interface 160k particle stack
 EMD-48259 consensus EM volume
Consensus refinement of 88k particle stack, shows improved density at VPS15/VPS34 interface
 EMD-48260 focused EM volume
Local refinment of the VPS34/VPS15 kinase/pseudokinase interface 88k particle stack, shows improved density at VPS15/VPS34 interface
 9mhg FULLOVERLAP EMDB EMD-48257 consensus EM volume
Consensus refinement of 160k particle stack
 EMDB EMD-48258 focused EM volume
Local refinment of the VPS34/VPS15 kinase/pseudokinase interface 160k particle stack
 EMDB EMD-48259 consensus EM volume
Consensus refinement of 88k particle stack, shows improved density at VPS15/VPS34 interface
 EMDB EMD-48260 focused EM volume
Local refinment of the VPS34/VPS15 kinase/pseudokinase interface 88k particle stack, shows improved density at VPS15/VPS34 interface
 EMDB EMD-48277 associated EM volume
Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation
 Phosphatidylinositol-3 kinase class III complex I bound to RAB1A Phosphatidylinositol-3 kinase class III complex I bound to RAB1A 0 1 2 3 4 5 Homo sapiens 0.384450 Phosphoinositide 3-kinase regulatory subunit 4 Homo sapiens 0.15880851599999998 1 Homo sapiens LEVO MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPTLPLTSYKQELEELKIRLNS AQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLNNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWN WVLLTDFASFKPTYLPEDNPADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKRLEAEDYLKQQRGNAFPEIF YTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHDLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALE LILHLAPRLSVEILLDRITPYLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKVVTLLSDPENIVKQTLMENG ITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSIVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALT CMCQLGLLQKPHVYEFASDIAPFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTEEEEDKLLALKDFMMKSNKA KANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPDDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSD QEVIQTGKPPRSESSAGICVPLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWNSQKMEGKTTTTRSILTYSR IGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPKIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGS LVGWDLRSSSNAWTLKHDLKSGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGSDMKIRFWDLAYPERSYVVA GSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGPESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKGT ENLYFQSGMAAWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDK Q99570 2.7.11.1 Phosphatidylinositol 3-kinase catalytic subunit type 3 Homo sapiens 0.10168032799999999 1 Homo sapiens LEVO MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVTCQVFAEGKPLALPVRTSYKA FSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAVPVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTP GRTSSTLSEDQMSRLAKLTKAHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFR YYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLV QALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQ RESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDD LRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRK QCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHK FAQYWRK Q8NEB9 2.7.1.137 Beclin 1-associated autophagy-related key regulator Homo sapiens 0.055387266 1 Homo sapiens LEVO MASPSGKGARALEAPGCGPRPLARDLVDSVDDAEGLYVAVERCPLCNTTRRRLTCAKCVQSGDFVYFDGRDRERFIDKKE RLSRLKSKQEEFQKEVLKAMEGKWITDQLRWKIMSCKMRIEQLKQTICKGNEEMEKNSEGLLKTKEKNQKLYSRAQRHQE KKEKIQRHNRKLGDLVEKKTIDLRSHYERLANLRRSHILELTSVIFPIEEVKTGVRDPADVSSESDSAMTSSTVSKLAEA RRTTYLSGRWVCDDHNGDTSISITGPWISLPNNGDYSAYYSWVEEKKTTQGPDMEQSNPAYTISAALCYATQLVNILSHI LDVNLPKKLCNSEFCGENLSKQKFTRAVKKLNANILYLCFSQHVNLDQLQPLHTLRNLMYLVSPSSEHLGRSGPFEVRAD LEESMEFVDPGVAGESDESGDERVSDEETDLGTDWENLPSPRFCDIPSQSVEVSQSQSTQASPPIASSSAGGMISSAAAS VTSWFKAYTGHR Q6ZNE5 Beclin-1 Homo sapiens 0.051953101999999994 1 Homo sapiens LEVO MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSR RFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQ NYKRCLEILEQMNEDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANK MGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEK GKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK Q14457 Ras-related protein Rab-1A Homo sapiens 0.025206526999999996 1 Escherichia coli BL21 LEVO MKSSHHHHHHENLYFQSNAMGMSSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKT IKLQIWDTAGLERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTA KEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMGPGATAGGAEKSNVKIQSTPVKQSGGGCC P62820 3.6.5.2 GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 2 GTP MAGNESIUM ION 2.4305e-05 2 MG MYRISTIC ACID 0.000228371 1 MYR singleParticle particle 0.2 7.4 25.0 C8H18N2O4S HEPES 200.0 NaCl sodium chloride 2.0 MgCl2 Magnesium chloride 1.0 C9H15O6P TCEP
OG supplemented at time of grid preparation 0.05%
 Quantifoil Active R2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE
25 mA
 ETHANE 100 281 FEI VITROBOT MARK IV
100% humidity, 3 s wait time, blot force -15.
monodisperse sample
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 19300 50.0 1 NONE 1 3.2 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 161381 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 3 cryoSPARC 3.3.1 emd_48277.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.19998 419.19998 419.19998 90.0 90.0 90.0 X Y Z -0.649076 1.660769 0.007180755 0.025703546 1.048 1.048 1.048 0.15 AUTHOR AlphaFold in silico model FLEXIBLE FIT ISOLDE 1.7 REAL