Focused map 4 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

2024-04-10 REL PDBe PDBe PDBe 2024-03-14 2024-04-10 2024-04-10 2024-04-10 Max Planck Society Germany Focused map 4 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide Liwocha J Prabu JR Kleiger G Schulman BA CUL2, FEM1C, ELOBC, SIL1, Ubiquitin, Ubiquitin Ligase, Ubiquitin chain formation, Poliubiquitylation, LIGASE Liwocha J Li J Purser N Rattanasopa C Maiwald S Krist DT Scott DC Steigenberger B Prabu JR Schulman BA Kleiger G Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Nat.Struct.Mol.Biol. US 31 378 389 2024 38326650 doi:10.1038/s41594-023-01206-1 1545-9985 EMD-17803 consensus EM volume

Consensus map - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

EMD-17822 other EM volume

K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

EMD-19856 focused EM volume

Focused map 1 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

EMD-19857 focused EM volume

Focused map 2 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

EMD-19858 focused EM volume

Focused map 3 - K48-linked ubiquitin chain formation with a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB~acceptor UB-SIL1 peptide

K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and CDC34:NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and CDC34:NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide 0 1 2 3 4 5 6 0.19 RING E3 ligase (RBX1) and Cullin-2 (CUL2) 1 4 6 Homo sapiens CDC34, NEDD8, FEM1C with UBE2R2-donor UB-acceptor UB-SIL1 peptide and K48-linked ubiquitin chain 1 1 2 3 5 Homo sapiens Ubiquitin-conjugating enzyme E2 R2 Homo sapiens 0.027190932 1 Escherichia coli BL21 LEVO MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTK MWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKE YAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPSNDNSSDLLYDDLYDDDIDDEDEEEEDADCYDDDDSGNEES 2.3.2.23 Polyubiquitin-C,Nucleotide exchange factor SIL1 Homo sapiens 0.07922671099999999 1 Escherichia coli BL21 LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLE VEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQD KEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGVEGYFQELLGSVNPTQGRAR Protein fem-1 homolog C Homo sapiens 0.068767312 1 Escherichia coli BL21 LEVO MDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVEFLLEQCSASIEVGGSVNFDGET IEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNSTPLRAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKG HKEIAQYLLEKGADVNRKSVKGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQTS KTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDYAKEVNSAEELEGLIADPDEMRM QALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCINLWKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKG LLGTTVTFDDLMGILCKSVLEIERAIKQTQCPADPLQLNKALSIILHLICLLEKVPCTLEQDHFKKQTIYRFLKLHPRGK NNFSPLHLAVDKNTTCVGRYPVCKFPSLQVTAILIECGADVNVRDSDDNSPLHIAALNNHPDIMNLLIKSGAHFDATNLH KQTASDLLDEKEIAKNLIQPINHTTLQCLAARVIVNHRIYYKGHIPEKLETFVSLHR E3 ubiquitin-protein ligase RBX1 Homo sapiens 0.012289977 1 Trichoplusia ni LEVO MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFH FHCISRWLKTRQVCPLDNREWEFQKYGH 2.3.2.27 Ubiquitin Homo sapiens 0.07712039799999999 1 Escherichia coli BL21 LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTL TGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKT ITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLE VEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIE NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKA KIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQD KEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGV Cullin-2 Homo sapiens 0.08709892999999999 1 Trichoplusia ni LEVO MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESE EQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILI RMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIH DEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLK KSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLC TGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSL NMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK CIEVLIDKQYIERSQASADEYSYVA singleParticle particle 7.5 ETHANE-PROPANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 2.6 GATAN K3 BIOQUANTUM (6k x 4k) 60.0 1 5N4W 3.89 FSC 0.143 CUT-OFF 55024 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_19859.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 -0.02933396 2.3979144 0.0006668821 0.019380046 0.8512 0.8512 0.8512 0.0682 AUTHOR ::::EMDATABANK.org::::EMD-19859:::: DeepEMhancer map emd_19859_msk_1.map emd_19859_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 -0.029064609 0.056617975 0.000032889544 0.00072893396 0.8512 0.8512 0.8512 AUTHOR ::::EMDATABANK.org::::EMD-19859:::: Postprocessed map emd_19859_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 -0.023339884 0.040551815 -0.000008464584 0.0014173208 0.8512 0.8512 0.8512 AUTHOR ::::EMDATABANK.org::::EMD-19859:::: emd_19859_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 -0.021267537 0.043832134 -0.000009173213 0.0014304811 0.8512 0.8512 0.8512 AUTHOR ::::EMDATABANK.org::::EMD-19859::::