VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit, primary map processed with CryoTEN

2026-06-10 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY citation citation_author em_admin pdbx_modification_feature struct_conn struct_conn_type _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update PDBe PDBe 2025-07-10 2026-06-03 2026-06-03 2026-06-10 Medical Research Council (MRC, United Kingdom) MC_U105184308 United Kingdom Cancer Research UK DRCPGM 100014 United Kingdom VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit, primary map processed with CryoTEN Spokaite S Ohashi Y Dessus AN Bourguet M Williams RL Lipid kinase, GTPase, kinase, endocytic trafficking, endosome maturation, SIGNALING PROTEIN, ENDOCYTOSIS Spokaite S Ohashi Y Bourguet M Dessus AN Williams RL A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution. Elife US 15 2026 42207670 doi:10.7554/eLife.110040 2050-084X Spokaite S Ohashi Y Bourguet M Dessus AN Williams RL A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution Elife US 2026 doi:10.7554/eLife.110040.3 2050-084X 9rx9 FULLOVERLAP EMDB EMD-54362 associated EM volume

VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit

Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) incubated with 22-fold molar excess of RAB5A-GTP (C19S, C63S, Q79L) Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) incubated with 22-fold molar excess of RAB5A-GTP (C19S, C63S, Q79L) 0 5 1 4 3

RAB5A is bound to the VPS34 subunit in this class

Homo sapiens 0.432 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 Phosphoinositide 3-kinase regulatory subunit 4 Homo sapiens 0.15465918799999998

Full length VPS15 with 13 extra residues at the C-terminus left after TEV cleavage (VPS35-SRPTTASENLYFQ)

1 Homo sapiens LEVO GNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPTLPLTSYKQELEELKIRLNSA QNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLNNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWNW VLLTDFASFKPTYLPEDNPADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMDI FSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKRLEAEDYLKQQRGNAFPEIFY TFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHDLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALEL ILHLAPRLSVEILLDRITPYLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRLA YAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKVVTLLSDPENIVKQTLMENGI TRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSIVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALTC MCQLGLLQKPHVYEFASDIAPFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVLK EPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTEEEEDKLLALKDFMMKSNKAK ANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPDDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSDQ EVIQTGKPPRSESSAGICVPLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERIA KQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWNSQKMEGKTTTTRSILTYSRI GGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPKIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGSL VGWDLRSSSNAWTLKHDLKSGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWVI AAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGSDMKIRFWDLAYPERSYVVAG STSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGPESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKSRP TTASENLYFQ Q99570 2.7.11.1 Beclin-1 Homo sapiens 0.051953101999999994

Full length BECLIN1

1 Homo sapiens LEVO MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSR RFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQ NYKRCLEILEQMNEDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANK MGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEK GKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK Q14457 UV radiation resistance associated protein Homo sapiens 0.078289852

Full length UVRAG with a P10Q mutation

1 Homo sapiens LEVO MSASASVGGQVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQLLDTYFTLHLCSTEKIYKEF YRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDG YYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCRQ LLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNIN DKLTEKEREFPLYPKGGEKLQFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGETERKITSLSSSLDTSLDFSKE NKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTLLPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEA TGFASGDQLEAFNCIPVDSAVAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK Q6P1X0 Ras-related protein Rab-5A Homo sapiens 0.023333225

RAB5A-GTP 1-212 construct, with C19S, C63S, Q79L mutations

1 Escherichia coli LEVO MASRGATRPNGPNTGNKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVSLDDTTVKFEIWDTAGLE RYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFM ETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANSARGRGVDLTEPTQPTRNQC P20339 3.6.5.2 GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP MAGNESIUM ION 2.4305e-05 2 MG MYRISTIC ACID 0.000228371 1 MYR ZINC ION 6.5409e-05 1 ZN GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 1 GTP singleParticle particle 1.5 8.0 50.0 C8H18N2O4S HEPES 200.0 NaCl Sodium chloride 1.0 C9H15O6P TCEP 5.0 MgCl2 Magnesium chloride 1.0 C10H17N6O12P3 AMPPNP 4.0 C32H58N2O8S CHAPSO 0.005 (C2H4O)nC14H22O Nonidet P40 substitute UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY GLOW DISCHARGE 90 AIR ETHANE 100 287 FEI VITROBOT MARK III

3.5 uL sample, 0 second wait, 4 second blot, blot force +8.

Sample was crosslinked with 20 uM BS3 for 20 minutes on ice, then quenched with 100 mM TRIS pH 8.0 prior to vitrification

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 0.8 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 2 19844 40.0 1 717560

crYOLO trained model was used

NONE

Density from VPS34-CI bound to NRBF2 MIT domain, determined earlier

3.99 FSC 0.143 CUT-OFF cryoSPARC 49688 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_54362.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 321.2 321.2 321.2 90.0 90.0 90.0 X Y Z -0.080685936 0.73662734 0.0013372366 0.017717434 0.73 0.73 0.73 0.11 AUTHOR ::::EMDATABANK.org::::EMD-54362:::: FLEXIBLE FIT REAL emd_54362_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 321.2 321.2 321.2 90.0 90.0 90.0 X Y Z -0.14321291 0.71010876 0.0036320586 0.026263148 0.73 0.73 0.73 AUTHOR ::::EMDATABANK.org::::EMD-54362:::: emd_54362_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 321.2 321.2 321.2 90.0 90.0 90.0 X Y Z -0.37173215 0.8151252 0.002379379 0.048763596 0.73 0.73 0.73 AUTHOR ::::EMDATABANK.org::::EMD-54362:::: emd_54362_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 321.2 321.2 321.2 90.0 90.0 90.0 X Y Z -0.3427596 0.8090849 0.0023355857 0.048925053 0.73 0.73 0.73 AUTHOR ::::EMDATABANK.org::::EMD-54362::::