2025-12-03 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.pdbx_database_id_PubMed _citation.title _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update RCSB RCSB 2025-05-13 2025-06-04 2025-06-04 2025-12-03 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) T32GM136614 United States National Science Foundation (NSF, United States) MCB-1714569 United States National Science Foundation (NSF, United States) DMR-1548924 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM128867 United States National Institutes of Health/National Center for Research Resources (NIH/NCRR) S10RR028893 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM145286 United States Department of Energy (DOE, United States) DE-FC02-02ER63421 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) T32GM145388 United States Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1) Pang EZ Zhao B Flowers C Oroudjeva E Winters JB Pandey V Sawaya MR Wohlschlegel W Loo JA Rodriguez JA Clarke SG CUL5-RING ubiquitin ligase complex, PROTEIN BINDING Pang EZ Zhao B Flowers C Oroudjeva E Winter JB Pandey V Sawaya MR Wohlschlegel J Loo JA Rodriguez JA Clarke SG Structural basis for L-isoaspartyl-containing protein recognition by the human PCMTD1 cullin-RING E3 ubiquitin ligase. J.Biol.Chem. US 301 110735 110735 2025 40975169 doi:10.1016/j.jbc.2025.110735 1083-351X 0071 JBCHA3 Pang EZ Zhao B Flowers C Oroudjeva E Winter JB Pandey V Sawaya MR Wohlschlegel J Loo JA Rodriguez JA Clarke SG Structural basis for L-isoaspartyl-containing protein recognition by the PCMTD1 cullin-RING E3 ubiquitin ligase. Biorxiv US 2025 40475564 doi:10.1101/2025.05.21.654933 2692-8205 EMD-70630 consensus EM volume EMD-70631 focused EM volume EMD-70632 focused EM volume EMD-70633 focused EM volume 9oma FULLOVERLAP EMDB EMD-70610 associated EM volume
Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)
 EMDB EMD-70630 consensus EM volume EMDB EMD-70631 focused EM volume EMDB EMD-70632 focused EM volume EMDB EMD-70633 focused EM volume Pentameric complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (CRL5-PCMTD1) Pentameric complex of PCMTD1, Elongins B and C, Cullin-5, and RING-box protein 2 (CRL5-PCMTD1) 0 1 2 3 4 5 Homo sapiens PCMTD1-ELOBC substrate receptor complex 1 1 4 5 Homo sapiens PCMTD1 2 1 Homo sapiens CUL5-RBX2 catalytic core 1 Homo sapiens Protein-L-isoaspartate O-methyltransferase domain-containing protein 1 Homo sapiens 0.04081434799999999 1 Escherichia coli LEVO SMGGAVSAGEDNDDLIDNLKEAQYIRTERVEQAFRAIDRGDYYLEGYRDNAYKDLAWKHGNIHLSAPCIYSEVMEALKLQ PGLSFLNLGSGTGYLSTMVGLILGPFGINHGIELHSDVVEYAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLQIASDSHQ YDRIYCGAGVQKDHENYMKILLKVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLVQPSKNDNGKPDSVGLPPCA VRNLQDLARIYIRRTLRNFINDEMQAKGIPQRAPPKRKRKRVKQRINTYVFVGNQLIPQPLDSEEDEKMEEDIKEEEEKD HNEAMKPEEPPQNLLREKIMKLPLPESLKAYLTYFRDK Q96MG8 Cullin-5 Homo sapiens 0.09143667999999999 1 Escherichia coli LEVO GEFMATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDILEFIKQAQ ARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQD SAMKLVHAERLGEAFDSQLVIGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAK LKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEPMLKDLEEH IISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKEAFQDDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLK TQPESKCPELLANYCDMLLRKTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMV EWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPE VEEFYKKNHYGRKLHWHHLMSNGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENVKLATELPDAELRRTLWSL VAFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQE AIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYILRDESDINTFIYMA Q93034 RING-box protein 2 Homo sapiens 0.0127215 1 Escherichia coli LEVO MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQEDCVVVWGEC NHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK Q9UBF6 2.3.2.27 Elongin-B Homo sapiens 0.013147781 1 Escherichia coli LEVO MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFR ADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ Q15370 Elongin-C Homo sapiens 0.01084342 1 Escherichia coli LEVO MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIA PEIALELLMAANFLDC Q15369 singleParticle particle 2.8 7.4 50.0 HEPES 150.0 sodium chloride 1.0 DTT SPT Labtech self-wicking R1.2/0.8 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE SPT LABTECH CHAMELEON
Sample was monodisperse and freshly gel-filtrated prior to sample vitrification
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 5447 2.1 50.0 1 1302046 NONE
Ab initio model generated in cryoSPARC
 4.14 FSC 0.143 CUT-OFF cryoSPARC 4 352937 MAXIMUM LIKELIHOOD cryoSPARC 4 MAXIMUM LIKELIHOOD cryoSPARC 4 emd_70610.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 412.80002 412.80002 412.80002 90.0 90.0 90.0 X Y Z -0.074688256 19.586130000000001 -0.021944184 0.23034644 0.86 0.86 0.86 3.0 AUTHOR Composite map of CRL5-PCMTD1 sharpened via EMReady A AlphaFold in silico model 6V9I B PDB experimental model
Initial model consisted of CUL5 from PDB entry 6V9I. Side-chain packing was performed with FASPR.
 6V9I C PDB experimental model
Initial model consisted of RBX2 from PDB entry 6V9I. Side-chain packing was performed with FASPR.
 8FVI D PDB experimental model
Initial model consisted of ELOB from PDB entry 8FVI
 8FVI E PDB experimental model
Initial model consisted of ELOC from PDB entry 8FVI
 OTHER
After initial fitting in ChimeraX, model was energy minimized against the 3D map with Rosetta FastRelax, adjusted in Coot, and refined in Phenix.
REAL