2024-05-01 REL PDBe PDBe PDBe 2021-01-17 2021-03-03 2021-03-03 2024-05-01 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 European Research Council (ERC) ERC-CoG-648432 MEMBRANEFUSION United Kingdom Wellcome Trust No. 103139 United Kingdom Wellcome Trust No. 203149 United Kingdom human complex II-BATS bound to membrane-attached Rab5a-GTP Tremel S Morado DR Rab GTPase, Phosphatidylinositol 3-kinase, ENDOCYTOSIS Tremel S Ohashi Y Morado DR Bertram J Perisic O Brandt LTL von Wrisberg MK Chen ZA Maslen SL Kovtun O Skehel M Rappsilber J Lang K Munro S Briggs JAG Williams RL Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Nat Commun UK 12 1564 1564 2021 33692360 doi:10.1038/s41467-021-21695-2 2041-1723 EMD-12237 other EM volume
EMD-12237 is the full density for the protein complex plus the membrane. It was resampled so that the current entry PDB entry fits the density.
 EMD-12238 other EM volume
This is a sample bin4 tomogram from which some subtomograms for this entry were extracted. This sample is not ctf corrected
 7bl1 FULLOVERLAP human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a 0 1 2 3 4 5 6
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)
392615 human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) 1 1 2 3 4 5 Homo sapiens Ras-related protein Rab-5A 1 6 Homo sapiens UV radiation resistance-associated gene protein Homo sapiens 0.078258836 1 Homo sapiens LEVO MSASASVGGPVPQPPPGPAAALPPGSAARALHVELPSQQRRLRHLRNIAARNIVNRNGHQLLDTYFTLHLCSTEKIYKEF YRSEVIKNSLNPTWRSLDFGIMPDRLDTSVSCFVVKIWGGKENIYQLLIEWKVCLDGLKYLGQQIHARNQNEIIFGLNDG YYGAPFEHKGYSNAQKTILLQVDQNCVRNSYDVFSLLRLHRAQCAIKQTQVTVQKIGKEIEEKLRLTSTSNELKKKSECL QLKILVLQNELERQKKALGREVALLHKQQIALQDKGSAFSAEHLKLQLQKESLNELRKECTAKRELFLKTNAQLTIRCRQ LLSELSYIYPIDLNEHKDYFVCGVKLPNSEDFQAKDDGSIAVALGYTAHLVSMISFFLQVPLRYPIIHKGSRSTIKDNIN DKLTEKEREFPLYPKGGEKLQFDYGVYLLNKNIAQLRYQHGLGTPDLRQTLPNLKNFMEHGLMVRCDRHHTSSAIPVPKR QSSIFGGADVGFSGGIPSPDKGHRKRASSENERLQYKTPPPSYNSALAQPVTTVPSMGETERKITSLSSSLDTSLDFSKE NKKKGEDLVGSLNGGHANVHPSQEQGEALSGHRATVNGTLLPSEQAGSASVQLPGEFHPVSEAELCCTVEQAEEIIGLEA TGFASGDQLEAFNCIPVDSAVAVECDEQVLGEFEEFSRRIYALNENVSSFRRPRRSSDK Q9P2Y5 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 0.154790391 1 Homo sapiens LEVO MGNQLAGIAPSQILSVESYFSDIHDFEYDKSLGSTRFFKVARAKHREGLVVVKVFAIQDPTLPLTSYKQELEELKIRLNS AQNCLPFQKASEKASEKAAMLFRQYVRDNLYDRISTRPFLNNIEKRWIAFQILTAVDQAHKSGVRHGDIKTENVMVTSWN WVLLTDFASFKPTYLPEDNPADFNYFFDTSRRRTCYIAPERFVDGGMFATELEYMRDPSTPLVDLNSNQRTRGELKRAMD IFSAGCVIAELFTEGVPLFDLSQLLAYRNGHFFPEQVLNKIEDHSIRELVTQMIHREPDKRLEAEDYLKQQRGNAFPEIF YTFLQPYMAQFAKETFLSADERILVIRKDLGNIIHNLCGHDLPEKAEGEPKENGLVILVSVITSCLQTLKYCDSKLAALE LILHLAPRLSVEILLDRITPYLLHFSNDSVPRVRAEALRTLTKVLALVKEVPRNDINIYPEYILPGIAHLAQDDATIVRL AYAENIALLAETALRFLELVQLKNLNMENDPNNEEIDEVTHPNGNYDTELQALHEMVQQKVVTLLSDPENIVKQTLMENG ITRLCVFFGRQKANDVLLSHMITFLNDKNDWHLRGAFFDSIVGVAAYVGWQSSSILKPLLQQGLSDAEEFVIVKALYALT CMCQLGLLQKPHVYEFASDIAPFLCHPNLWIRYGAVGFITVVARQISTADVYCKLMPYLDPYITQPIIQIERKLVLLSVL KEPVSRSIFDYALRSKDITSLFRHLHMRQKKRNGSLPDCPPPEDPAIAQLLKKLLSQGMTEEEEDKLLALKDFMMKSNKA KANIVDQSHLHDSSQKGVIDLAALGITGRQVDLVKTKQEPDDKRARKHVKQDSNVNEEWKSMFGSLDPPNMPQALPKGSD QEVIQTGKPPRSESSAGICVPLSTSSQVPEVTTVQNKKPVIPVLSSTILPSTYQIRITTCKTELQQLIQQKREQCNAERI AKQMMENAEWESKPPPPGWRPKGLLVAHLHEHKSAVNRIRVSDEHSLFATCSNDGTVKIWNSQKMEGKTTTTRSILTYSR IGGRVKTLTFCQGSHYLAIASDNGAVQLLGIEASKLPKSPKIHPLQSRILDQKEDGCVVDMHHFNSGAQSVLAYATVNGS LVGWDLRSSSNAWTLKHDLKSGLITSFAVDIHQCWLCIGTSSGTMACWDMRFQLPISSHCHPSRARIRRLSMHPLYQSWV IAAVQGNNEVSMWDMETGDRRFTLWASSAPPLSELQPSPHSVHGIYCSPADGNPILLTAGSDMKIRFWDLAYPERSYVVA GSTSSPSVSYYRKIIEGTEVVQEIQNKQKVGPSDDTPRRGPESLPVGHHDIITDVATFQTTQGFIVTASRDGIVKVWKSR PTTASENLYFQ Q99570 2.7.11.1 Beclin-1 Homo sapiens 0.051953101999999994 1 Homo sapiens LEVO MEGSKTSNNSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSR RFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQ NYKRCLEILEQMNEDDSEQLQMELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQ LELDDELKSVENQMRYAQTQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANK MGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEK GKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQFYNK Q14457 unknown peptide Homo sapiens 0.001581727 1 Homo sapiens LEVO AAAAAAAAAAAAAAAAAAAAAA Ras-related protein Rab-5A Homo sapiens 0.018769314 1 Escherichia coli str. K-12 substr. DH10B LEVO NKISQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVSLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQA AIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFM AIAKKLPK P20339 3.6.5.2 GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 1 GTP MAGNESIUM ION 2.4305e-05 1 MG subtomogramAveraging 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 20, blot time 6 s.
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 BIOQUANTUM (6k x 4k) 6000 4000 1 0.55 2.99 1 C1 FOURIER SPACE 9.8 FSC 0.143 CUT-OFF RELION 3.1 26979 105 191196 two Gaussian filtered elipsoids MATLAB R2016b The locally written subTOM 20 9600.0 MATLAB R2016b locally written subTOM PROJECTION MATCHING correlation coefficient MATLAB R2016b locally written subTOM emd_12214.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 341.27997 341.27997 341.27997 90.0 90.0 90.0 X Y Z -0.045468677 0.06802449 0.00014741789 0.002034834 1.0665 1.0665 1.0665 0.008 AUTHOR Subtomogram averaging reconstruction of human complex II-BATS bound to membrane-attached Rab5a-GTP at 9.8A with the membrane masked out after local-denoising with the LAFTER algorithm 5DFZ PDB experimental model 3MJH A PDB experimental model 4DDP A PDB experimental model 3IHY A PDB experimental model FLEXIBLE FIT
An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY.
correlation REAL 320.0 emd_12214_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 341.27997 341.27997 341.27997 90.0 90.0 90.0 X Y Z -0.1647642 0.26415938 0.00054734887 0.016963452 2.133 2.133 2.133 AUTHOR Odd Half-map masked to remove density from the membrane. emd_12214_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 341.27997 341.27997 341.27997 90.0 90.0 90.0 X Y Z -0.17500676 0.26356658 0.0005375241 0.016816692 2.133 2.133 2.133 AUTHOR Even Half-map masked to remove density from the membrane.