9OMA: PCMTD1-ELOBC-CUL5-RBX2

Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1). Determined by electron microscopy at 4.14 Å resolution. Released 4 Jun 2025.

Method
Electron microscopy
Resolution
4.14 Å
Organism
Homo sapiens
Chains
5
Atoms
10,325
Mol. weight
168.96 kDa
Released
4 Jun 2025

Explore 9OMA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OMA contains 68 α-helices and 47 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix11-2010
α-helix27-359
α-helix49-513
β-strand57-5821
β-strand61-6221
α-helix67-759
β-strand83-8752
α-helix93-10210
β-strand107-11262
α-helix115-13117
α-helix135-1373
β-strand144-14742
β-strand160-16562
β-strand16813
β-strand16912
α-helix171-1733
α-helix174-1785
β-strand181-191112
β-strand194-20072
β-strand206-21382
α-helix2171
β-strand21813
α-helix2191
α-helix235-2384
α-helix243-26321
α-helix332-3376
α-helix343-3453
α-helix346-3505
Chain B: 42 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix22-309
α-helix37-5216
α-helix61-8121
α-helix86-10419
α-helix134-14310
α-helix144-1485
α-helix149-16719
α-helix175-18713
α-helix197-1982
α-helix199-2035
α-helix204-21714
α-helix219-2224
α-helix227-24822
α-helix257-26913
α-helix271-2733
α-helix274-2774
α-helix278-2803
α-helix281-2866
α-helix290-30011
α-helix308-33225
α-helix337-35822
α-helix363-37715
α-helix407-41610
β-strand41714
α-helix420-4234
α-helix427-44115
α-helix449-46416
β-strand46714
α-helix470-48314
α-helix487-4904
α-helix492-51322
α-helix523-5253
β-strand52815
β-strand531-53226
α-helix533-5364
α-helix549-5524
α-helix555-56410
β-strand570-57346
β-strand579-58577
β-strand590-59677
α-helix597-60711
β-strand614-61528
α-helix616-6238
α-helix627-63812
β-strand648-65038
α-helix657-6593
β-strand665-66848
β-strand675-67629
β-strand679-68029
β-strand685-68737
α-helix690-6934
α-helix697-72529
β-strand728-730310
α-helix731-74111
α-helix742-7443
α-helix750-76213
β-strand767-768210
β-strand775-777310
Chain C: 3 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand3617
β-strand3715
β-strand39-4246
α-helix63-664
β-strand75-77311
β-strand83-85311
α-helix89-924
β-strand98112
β-strand105112
α-helix106-1083
Chain D: 3 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand5-9513
β-strand10114
β-strand12-16513
α-helix24-3512
β-strand46115
β-strand49115
α-helix64-663
β-strand68116
β-strand71116
α-helix721
β-strand73-75313
β-strand90114
Chain E: 4 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand2-6513
β-strand12-16513
α-helix17-204
α-helix24-285
β-strand43-45313
α-helix51-6717
α-helix84-918

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein-L-isoaspartate O-methyltransferase domain-containing protein 1Aprotein358Homo sapiensQ96MG8 (AlphaFold model)
Cullin-5Bprotein783Homo sapiensQ93034 (AlphaFold model)
RING-box protein 2Cprotein113Homo sapiensQ9UBF6 (AlphaFold model)
Elongin-BDprotein118Homo sapiensQ15370 (AlphaFold model)
Elongin-CEprotein96Homo sapiensQ15369
Sequence of entity 1 (A), FASTA
>9OMA_1 Protein-L-isoaspartate O-methyltransferase domain-containing protein 1 (chains A)
SMGGAVSAGEDNDDLIDNLKEAQYIRTERVEQAFRAIDRGDYYLEGYRDNAYKDLAWKHG
NIHLSAPCIYSEVMEALKLQPGLSFLNLGSGTGYLSTMVGLILGPFGINHGIELHSDVVE
YAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLQIASDSHQYDRIYCGAGVQKDHENYMKI
LLKVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLVQPSKNDNGKPDSVGLPPCA
VRNLQDLARIYIRRTLRNFINDEMQAKGIPQRAPPKRKRKRVKQRINTYVFVGNQLIPQP
LDSEEDEKMEEDIKEEEEKDHNEAMKPEEPPQNLLREKIMKLPLPESLKAYLTYFRDK
Sequence of entity 2 (B), FASTA
>9OMA_2 Cullin-5 (chains B)
GEFMATSNLLKNKGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKG
PAKIHQALKEDILEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEIT
LMGKQGSNKKSNVEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLV
IGVRESYVNLCSNPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAK
LKEEEKRALRYLETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMF
SLMDKVPNGIEPMLKDLEEHIISAGLADMVAAAETITTDSEKYVEQLLTLFNRFSKLVKE
AFQDDPRFLTARDKAYKAVVNDATIFKLELPLKQKGVGLKTQPESKCPELLANYCDMLLR
KTPLSKKLTSEEIEAKLKEVLLVLKYVQNKDVFMRYHKAHLTRRLILDISADSEIEENMV
EWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNKLALPADSVNIKILNAGAWS
RSSEKVFVSLPTELEDLIPEVEEFYKKNHYGRKLHWHHLMSNGIITFKNEVGQYDLEVTT
FQLAVLFAWNQRPREKISFENVKLATELPDAELRRTLWSLVAFPKLKRQVLLYEPQVNSP
KDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTERMREEENEGIVQLRILRTQE
AIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIEWLIEHKYILRDESDINTFI
YMA
Sequence of entity 3 (C), FASTA
>9OMA_3 RING-box protein 2 (chains C)
MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDA
CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
Sequence of entity 4 (D), FASTA
>9OMA_4 Elongin-B (chains D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 5 (E), FASTA
>9OMA_5 Elongin-C (chains E)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Primary citation

Structural basis for L-isoaspartyl-containing protein recognition by the human PCMTD1 cullin-RING E3 ubiquitin ligase. Pang, E.Z., Zhao, B., Flowers, C. et al. J Biol Chem (2025) 301:110735-110735. DOI 10.1016/j.jbc.2025.110735 · PubMed

Other PDB entries of the same protein (UniProt Q96MG8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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