2026-06-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update PDBe PDBe 2025-07-25 2026-06-03 2026-06-03 2026-06-17 Medical Research Council (MRC, United Kingdom) MC_U105184308 United Kingdom Cancer Research UK DRCPGM 100014 United Kingdom Human complex II-BATS bound to membrane-attached Rab5a-GTP Dessus AN Tremel S Williams RL Lipid kinase, kinase, 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 EMD-12214 other EM volume
Previously processed data. Human complex II-BATS bound to membrane-attached Rab5a-GTP, 3D cryo-ET map with the membrane masked-out before B-factor sharpening in LAFTER
 EMD-12237 other EM volume
Previously processed data. Human complex II-BATS bound to membrane-attached Rab5a-GTP, a reconstruction in which the lipid membrane was not masked-out before sharpening in LAFTER
 EMD-12238 other EM volume
a sample non-CTF-corrected bin4 tomogram
 9s47 FULLOVERLAP EMDB EMD-12214 other EM volume
Previously processed data. Human complex II-BATS bound to membrane-attached Rab5a-GTP, 3D cryo-ET map with the membrane masked-out before B-factor sharpening in LAFTER
 EMDB EMD-12237 other EM volume
Previously processed data. Human complex II-BATS bound to membrane-attached Rab5a-GTP, a reconstruction in which the lipid membrane was not masked-out before sharpening in LAFTER
 EMDB EMD-12238 other EM volume
a sample non-CTF-corrected bin4 tomogram
 EMDB EMD-54560 associated EM volume
Human complex II-BATS bound to membrane-attached Rab5a-GTP
 PDB 7BL1 unspecified
Model to be superseded by this deposition. Human complex II-BATS bound to membrane-attached Rab5a-GTP
 VPS34-CII-BATS bound to membrane-attached RAB5A-GTP (C19S, C63S, Q79L) on a LUV membrane VPS34-CII-BATS bound to membrane-attached RAB5A-GTP (C19S, C63S, Q79L) on a LUV membrane 0 1 2 3 4 5
RAB5A-GTP is attached to the LUV membrane via a maleimide linkage
Homo sapiens 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
UV radiation resistance associated protein (UVRAG; 1-464, with a P10Q mutation) fused to ATG14L BATS domain (413-492)UVRAG(1-464, P10Q) fused to ATG14L BATS domain (413-492)
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 MYRISTIC ACID 0.000228371 1 MYR GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP MAGNESIUM ION 2.4305e-05 2 MG ZINC ION 6.5409e-05 1 ZN GUANOSINE-5'-TRIPHOSPHATE 0.0005231799999999999 1 GTP subtomogramAveraging particle 8.0 50.0 C8H18N2O4S HEPES 200.0 NaCl NaCl 0.5 C9H15O6P TCEP Quantifoil GOLD 300 CARBON HOLEY ARRAY GLOW DISCHARGE AIR ETHANE 100 316 FEI VITROBOT MARK I TFS 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) 0.55 2.99 1 2 C1 FOURIER SPACE 9.88 FSC 0.143 CUT-OFF RELION 5.0 beta4-commit-dfea29 8441 103 146464 EMD-12237 crYOLO 1.9.9 RELION 5.0 beta4-commit-dfea29
Particles picked in crYOLO, using the crYOLO model trained for SPA data that was re-trained on 3 manually picked tomograms. Then, did a 3D classification on all particles with EMD-12237 as a reference (low-passed to 60A).
 CTFFIND 4.1 RELION 5.0 beta4-commit-dfea29
CTF estimated with CTFFIND-4.1 (wrapper in Relion5), then corrected during 3D refinement and CTF tomo refine in Relion5.
PHASE FLIPPING AND AMPLITUDE CORRECTION 2 8441.0 RELION 5.0 beta4-commit-dfea29 MAXIMUM LIKELIHOOD RELION 5.0 beta4-commit-dfea29 emd_54560.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 374.88 374.88 374.88 90.0 90.0 90.0 X Y Z -0.024605194 0.07123116 0.00048046513 0.005867256 2.13 2.13 2.13 0.017 AUTHOR human complex II-BATS bound to membrane-attached Rab5a-GTP, map with membrane masked out. 9RX9 PDB experimental model FLEXIBLE FIT cross-correlation coefficient REAL emd_54560_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 374.88 374.88 374.88 90.0 90.0 90.0 X Y Z -0.020524945 0.03696773 0.00058801984 0.0048085256 2.13 2.13 2.13 AUTHOR human complex II-BATS bound to membrane-attached Rab5a-GTP, map with membrane NOT masked out. emd_54560_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 374.88 374.88 374.88 90.0 90.0 90.0 X Y Z -0.11623748 0.15967996 0.00046451547 0.016769009 2.13 2.13 2.13 AUTHOR human complex II-BATS bound to membrane-attached Rab5a-GTP, map with membrane masked out. Half map B. emd_54560_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 176 176 176 0 0 0 176 176 176 374.88 374.88 374.88 90.0 90.0 90.0 X Y Z -0.11971771 0.15943895 0.0005032131 0.016816897 2.13 2.13 2.13 AUTHOR human complex II-BATS bound to membrane-attached Rab5a-GTP, map with membrane masked out. Half map A.