2025-12-24 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 INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_validate_close_contact struct_conn _em_admin.last_update STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight PDBe PDBe 2023-11-16 2024-02-21 2024-02-21 2025-12-24 Max Planck Society Germany Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Liwocha J Prabu JR Kleiger G Schulman BA CUL2, VHL, ELOBC, BRD4, MZ1, PROTAC, Ubiquitin, Ubiquitin Ligase, Monoubiquitylation, LIGASE, NEDD8, RBX1 Li J Purser N Liwocha J Scott DC Byers HA Steigenberger B Hill S Tripathi-Giesgen I Hinkle T Hansen FM Prabu JR Radhakrishnan SK Kirkpatrick DS Reichermeier KM Schulman BA Kleiger G Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol.Cell US 84 1304 2024 38382526 doi:10.1016/j.molcel.2024.01.022 1097-2765 2168 MOCEFL EMD-18207 other EM volume
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide, Glacios map
 EMD-18230 other EM volume
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
 8r5h FULLOVERLAP EMDB EMD-18207 other EM volume
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide, Glacios map
 EMDB EMD-18230 other EM volume
Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide
 EMDB EMD-18915 associated EM volume
Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2
 Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 0 1 2 3 4 5 6 7 8 Homo sapiens 0.19 RING E3 ligase (RBX1) and Cullin-2 (CUL2) 1 1 2 Homo sapiens CDC34, NEDD8, ELOB, ELOC, VHL, BRD4 with UBE2R2-donor UB- BRD4 BD2 1 3 4 5 6 7 8 Homo sapiens Cullin-2 Homo sapiens 0.08709892999999999 1 Trichoplusia ni LEVO MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESE EQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILI RMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIH DEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLK KSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSL NMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK CIEVLIDKQYIERSQASADEYSYVA Q13617 E3 ubiquitin-protein ligase RBX1, N-terminally processed Homo sapiens 0.011945547 1 Trichoplusia ni LEVO MDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCI SRWLKTRQVCPLDNREWEFQKYGH P62877 Ubiquitin-conjugating enzyme E2 R2 Homo sapiens 0.025853664 1 Escherichia coli BL21 LEVO MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTK MWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKE YAEIIRKQVSATKAEAEKDGVKVPTTLAEYCI(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) Q712K3 2.3.2.23 Ubiquitin Homo sapiens 0.008519778 1 Escherichia coli BL21 LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG P0CG48 Elongin-C Homo sapiens 0.012485135 1 Escherichia coli BL21 LEVO MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYK VRYTNSSTEIPEFPIAPEIALELLMAANFLDC Q15369 Bromodomain-containing protein 4 Homo sapiens 0.013256254 1 Escherichia coli BL21 LEVO KSSKVSEQLKAASGILKEMFAKCHAAYAWPFYKPVDVEALGLHDYADIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLM FSNAYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE O60885 Elongin-B Homo sapiens 0.013147781 1 Escherichia coli BL21 LEVO MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR ADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ Q15370 von Hippel-Lindau disease tumor suppressor Homo sapiens 0.018558162 1 Escherichia coli BL21 LEVO MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQT ELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD P40337 ZINC ION 6.5409e-05 3 ZN 5-azanylpentan-2-one 0.000101147 1 SY8 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide 0.001002639 1 759 singleParticle particle 7.5 ETHANE-PROPANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.6 130000.0 GATAN K3 BIOQUANTUM (6k x 4k) 66.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 8PQL C1 3.44 FSC 0.143 CUT-OFF 148402 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_18915.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.019646084 1.904623 0.00077119365 0.018465092 0.8512 0.8512 0.8512 0.0319 AUTHOR Consensus map from deepEMhancer emd_18915_msk_1.map emd_18915_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.01318097 0.0410298 0.000038099788 0.0009867956 0.8512 0.8512 0.8512 AUTHOR Refined map, where tail tube is visible emd_18915_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.046222433 1.8971711 0.0005887416 0.015648635 0.8512 0.8512 0.8512 AUTHOR Focused map from deepEMhancer emd_18915_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.028148284 0.05094654 0.00003751426 0.0007919427 0.8512 0.8512 0.8512 AUTHOR Consensus map postprocessed emd_18915_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.021926034 0.044772483 0.0000064090677 0.0014402507 0.8512 0.8512 0.8512 AUTHOR emd_18915_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 0 0 0 380 380 380 323.456 323.456 323.456 90.0 90.0 90.0 X Y Z -0.021894528 0.045465987 0.000007777597 0.0014353249 0.8512 0.8512 0.8512 AUTHOR