2024-10-02 REL PDBe PDBe PDBe 2023-10-14 2023-12-06 2023-12-06 2024-10-02 Other private Boehringer Ingelheim Austria Fischer G Peter D Arce-Solano S TARGETED PROTEIN DEGRADATION, PROTAC, GTPASE, TRANSFERASE Popow J Farnaby W Gollner A Kofink C Fischer G Wurm M Zollman D Wijaya A Mischerikow N Hasenoehrl C Prokofeva P Arnhof H Arce-Solano S Bell S Boeck G Diers E Frost AB Goodwin-Tindall J Karolyi-Oezguer J Khan S Klawatsch T Koegl M Kousek R Kratochvil B Kropatsch K Lauber AA McLennan R Olt S Peter D Petermann O Roessler V Stolt-Bergner P Strack P Strauss E Trainor N Vetma V Whitworth C Zhong S Quant J Weinstabl H Kuster B Ettmayer P Ciulli A Science US 385 1338 1347 2024 39298590 doi:10.1126/science.adm8684 1095-9203 0038 SCIEAS Popow J Farnaby W Gollner A Kofink C Fischer G Wurm M Zollman D Wijaya A Mischerikow N Hasenoehrl C Prokofeva P Arnhof H Arce-Solano S Bell S Boeck G Diers E Frost A Goodwin-Tindall J Karolyi-Oezguer J Khan S Klawatsch T Koegl M Kousek R Kratochvil B Kropatsch K Lauber A McLennan R Olt S Peter D Petermann O Roessler V Stolt-Bergner P Strack P Strauss E Trainor N Vetma V Whitworth C Zhong S Quant J Weinstabl H Kuster B Ettmayer P Ciulli A Biorxiv US 2023 doi:10.1101/2023.10.24.563163 2692-8205 8qu8 FULLOVERLAP KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1 KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1 0 1 2 3 4 5 6

PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1

Homo sapiens 0.168 von Hippel-Lindau disease tumor suppressor Homo sapiens 0.024049545 1 Escherichia coli LEVO PRRAENWDEAEVGAEEAGVEEYGPEEDGGEESGAEESGPEESGPEELGAEEEMEAGRPRPVLRSVNSREPSQVIFCNRSP RVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD P40337 Elongin-B Homo sapiens 0.013016585999999998 1 Escherichia coli LEVO DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRA DDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ Q15370 Elongin-C Homo sapiens 0.012353939 1 Escherichia coli LEVO DGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKV RYTNSSTEIPEFPIAPEIALELLMAANFLDC Q15369 Cullin-2 Homo sapiens 0.08696773399999999 1 Escherichia coli LEVO SLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEE QVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIR MLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLG RLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHD EGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKK SAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMS VSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCT GEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLN MNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKC IEVLIDKQYIERSQASADEYSYVA Q13617 E3 ubiquitin-protein ligase RBX1, N-terminally processed Homo sapiens 0.01215878 1 Escherichia coli LEVO AAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHF HCISRWLKTRQVCPLDNREWEFQKYGH P62877 GTPase KRas Homo sapiens 0.019354824 1 Escherichia coli LEVO GMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFL CVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTL VREIRKHKEK P01116 3.6.5.2 ZINC ION 6.5409e-05 2 ZN GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide 0.0010192469999999998 1 WYL singleParticle particle 0.916 7.5 50.0 TRIS 100.0 NaCl 0.5 TCEP 2.0 MgCl2 Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE 15 AIR ETHANE 95 4 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.8 2.0 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER TFS Selectris 10 FEI FALCON IV (4k x 4k) 1 7634 40.0 1 2414442

before 2D classification

cryoSPARC ab-initio

3.5 OTHER cryoSPARC 4 3Dflex reconstruction

cryoSPARC 3Dflex reconstruction

217000 MAXIMUM LIKELIHOOD cryoSPARC 3 MAXIMUM LIKELIHOOD cryoSPARC 3 3 162900.0 cryoSPARC 3 5n4w F PDB experimental model

KRAS-structure

emd_18657_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 381.44 381.44 381.44 90.0 90.0 90.0 X Y Z -0.013667012 0.031746715 0.000027085667 0.00044267657 0.99333334 0.99333334 0.99333334 AUTHOR ::::EMDATABANK.org::::EMD-18657:::: unsharpened map from 3D flex emd_18657_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 381.44 381.44 381.44 90.0 90.0 90.0 X Y Z -0.017423917 0.037344735 0.00002705768 0.0005725405 0.99333334 0.99333334 0.99333334 AUTHOR ::::EMDATABANK.org::::EMD-18657:::: half map A emd_18657_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 381.44 381.44 381.44 90.0 90.0 90.0 X Y Z -0.018808628 0.038873605 0.000027035407 0.00057434454 0.99333334 0.99333334 0.99333334 AUTHOR ::::EMDATABANK.org::::EMD-18657:::: half map B