Sample bin4 tomogram for the VPS34 complex II on Rab5a coupled lipid vesicles

2021-06-16 REL PDBe PDBe PDBe 2021-01-24 2021-06-16 2021-06-16 2021-06-16 Medical Research Council (MRC, United Kingdom) MC_U105184308 United Kingdom Medical Research Council (MRC, United Kingdom) MC_U10517878 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/16 United Kingdom Cancer Research UK C14801/A21211 United Kingdom European Research Council (ERC) ERC-CoG-648432 United Kingdom German Research Foundation (DFG) Sonderforschungsbereich 1035, project number 201302640, project B10 Germany German Research Foundation (DFG) 392923329 Germany Wellcome Trust 103139 United Kingdom Wellcome Trust 203149 United Kingdom Sample bin4 tomogram for the VPS34 complex II on Rab5a coupled lipid vesicles Tremel S Ohashi Y Morado DR Bertram J Perisic O Brandt LTL von Wrisberg M-K Chen ZA Maslen SL Kovtun O Skehel M Rappsilber J Lang K Munro S Briggs JAG Williams RL Tremel S Ohashi Y Morado DR Bertram J Perisic O Brandt LTL von Wrisberg M-K Chen ZA Maslen SL Skehel M Rappsilber J Lang K Munro S Briggs JAG Williams RL Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes To Be Published 0353 EMD-12214 other EM volume

This is a subtomogram averaged reconstruction of the VPS34 complex II on a Rab5a-linked membrane. Thelipid membrane was masked out.

EMD-12238 associated EM volume EMD-12237 other EM volume

This is a subtomogram averaged reconstruction of the VPS34 complex II on a Rab5a-linked membrane. Thelipid membrane was not masked out.

human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a on lipid vesicles 0 1 2 3 4 5

The subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 (encoding UVGRAG 1-464 fused to the BATS of ATG14, residues 413-492 in pVAG) and pYO1006 (Beclin1 in pCAG)

Homo sapiens Homo sapiens 0.39216 UV radiation resistance-associated gene protein Homo sapiens

Human UVRAG

Homo sapiens LEVO MSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQLLDTYFTLHLCSTEKIYKEF YRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDG YYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCRQ LLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNIN DKLTEKEREFPLYPKGGEKLQFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGETERKITSLSSSLDTSLDFSKE NKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTLLPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEA TGFASGDQLEAFNCIPVDSAVAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK 2.7.1.137 Phosphatidylinositol 3-kinase catalytic subunit type 3 Homo sapiens

human vps34

Homo sapiens LEVO MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVTCQVFAEGKPLALPVRTSYKA FSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAVPVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTP GRTSSTLSEDQMSRLAKLTKAHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIVSYPPTKQLTYEEQDLVWKFR YYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLV QALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQ RESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDD LRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRK QCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHK FAQYWRK 2.7.1.137 Phosphoinositide 3-kinase regulatory subunit 4 Homo sapiens Homo sapiens LEVO MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPTLPLTSYKQELEELKIRLNS AQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLNNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWN WVLLTDFASFKPTYLPEDNPADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKRLEAEDYLKQQRGNAFPEIF YTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHDLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALE LILHLAPRLSVEILLDRITPYLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKVVTLLSDPENIVKQTLMENG ITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSIVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALT CMCQLGLLQKPHVYEFASDIAPFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTEEEEDKLLALKDFMMKSNKA KANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPDDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSD QEVIQTGKPPRSESSAGICVPLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWNSQKMEGKTTTTRSILTYSR IGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPKIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGS LVGWDLRSSSNAWTLKHDLKSGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGSDMKIRFWDLAYPERSYVVA GSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGPESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKSR PTTASENLYFQ Beclin-1 Homo sapiens

Beclin1

Homo sapiens LEVO MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSR RFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQ NYKRCLEILEQMNEDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANK MGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEK GKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK Ras-related protein Rab-5A Homo sapiens Escherichia coli LEVO NKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVSLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQA AIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFM AIAKKLPK 3.6.5.2 tomography threeDArray 6.2 8.0 50.0 HEPES HEPES 200.0 NaCl NaCl 0.5 TCEP TCEP Quantifoil GOLD 300 CARBON HOLEY ARRAY GLOW DISCHARGE AIR

Quorum SC7620

ETHANE 100 316 FEI VITROBOT MARK I

blot force was 20, with a blot time of 6 s.

Large unilamellar lipid vesicles containing lipid-modified Rab5A to which VPS34 complex II is bound. 50 mM HEPES, 200 mM NaCl, 0.5 mM TCEP, 6 mg/ml lipid vesicles.

BBI Solutions EM 10 None NO SECTIONING FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 2.0 5.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 6000 4000 2.133 1 0.55 2.99 1 SIMULTANEOUS ITERATIVE (SIRT) IMOD 4.10 41 NOVACTF emd_12238.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1023 1440 250 -209 0 42 1023 1440 250 8728.235 12286.079 2133.0 90.0 90.0 90.0 X Y Z -9405.448 8169.91 63.60837 538.5632 8.532 8.532 8.532 AUTHOR ::::EMDATABANK.org::::EMD-12238:::: Sample tomogram before ctf correction. This is one of the tomograms used in END-12214 subtomogram average reconstruction.