2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2026-01-22 2026-08-05 2026-08-05 2026-09-16 Medical Research Council (MRC, United Kingdom) MC_U105184308 United Kingdom Cancer Research UK DRCPGM 100014 United Kingdom Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on VPS34 and VPS15 kinases Dessus AN Williams RL Lipid kinase, Complex, Autophagy, LIPID BINDING PROTEIN Dessus AN Ohashi Y Bourguet M Morgan TE Nunez A Manifava M Ktistakis NT Williams RL A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation. Nat Commun UK 17 2026 42693081 doi:10.1038/s41467-026-76135-w 2041-1723 EMDB EMD-56456 associated EM volume Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3 Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3 0 1 2 3 4 5 Homo sapiens 0.14086 Human VPS34-CI 1 1 2 3 4 Homo sapiens NRBF2 MIT domain 1 5 Homo sapiens singleParticle particle 1.35 8.0 25.0 HEPES HEPES 100.0 NaCl sodium chloride 1.0 TCEP Tris-(2-Carboxyethyl)phosphine 4.0 CHAPSO CHAPSO 0.005 Nonidet-P-40 Nonidet P-40 UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE AIR ETHANE 95 287.15 FEI VITROBOT MARK II
3.6 uM VPS34-CI was mixed with 3.6 uM NRBF2 MIT, in presence of 13 mM MgCl2, 22.5 mM NaF and 2.5 mM ADP.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.8 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 4092 5760 1 8483 1.66 50.0 1 306134 cryoSPARC 4.6.2 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-56346 3.33 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 55269 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 cryoSPARC 4.6.2 1 306134 cryoSPARC 4.6.2 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-56346 3.33 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 55269 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 cryoSPARC 4.6.2 emd_56456.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 452 452 452 0 0 0 452 452 452 327.7 327.7 327.7 90.0 90.0 90.0 X Y Z -0.39899093 0.6419037 0.00042846316 0.013663192 0.725 0.725 0.725 0.0755 AUTHOR 9TW2 PDB experimental model
GABARAP chain F was removed
 REAL emd_56456_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 452 452 452 0 0 0 452 452 452 327.7 327.7 327.7 90.0 90.0 90.0 X Y Z -0.9307383 1.0988572 0.0003108583 0.114618436 0.725 0.725 0.725 AUTHOR emd_56456_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 452 452 452 0 0 0 452 452 452 327.7 327.7 327.7 90.0 90.0 90.0 X Y Z -0.9948435 1.0566694 0.00031289758 0.113754295 0.725 0.725 0.725 AUTHOR