9OMF: Neddylated PCMTD1-ELOBC-CUL5-RBX2

Cryo-EM structure of neddylated PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5-PCMTD1). Determined by electron microscopy at 9.72 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 9.72 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 10,300
Mol. weight: 168.96 kDa
Released: 4 Jun 2025

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

Secondary structure: helices and β-sheets

9OMF contains 64 α-helices and 46 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: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	28-35	8
α-helix	37	1
α-helix	49-51	3
β-strand	58	1	1
β-strand	61	1	1
α-helix	67-75	9
β-strand	83-87	5	2
α-helix	93-101	9
β-strand	107-112	6	2
α-helix	115-131	17
α-helix	135-137	3
β-strand	144-147	4	2
β-strand	160-165	6	2
β-strand	168	1	3
β-strand	169	1	2
α-helix	171-173	3
α-helix	175-178	4
β-strand	181-191	11	2
β-strand	194-200	7	2
β-strand	206-213	8	2
α-helix	217	1
β-strand	218	1	3
α-helix	219	1
α-helix	243-262	20
α-helix	332-335	4
α-helix	343-349	7

Chain B: 39 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	23-30	8
α-helix	37-52	16
α-helix	57-81	25
α-helix	86-103	18
α-helix	134-146	13
α-helix	148-166	19
α-helix	175-186	12
α-helix	197-198	2
α-helix	199-204	6
α-helix	205-217	13
α-helix	219-222	4
α-helix	227-248	22
α-helix	257-266	10
α-helix	267-271	5
α-helix	272-286	15
α-helix	293-300	8
α-helix	304-333	30
α-helix	337-358	22
α-helix	363-373	11
α-helix	407-416	10
β-strand	417	1	4
α-helix	420-424	5
α-helix	427-441	15
β-strand	446	1	5
α-helix	448-464	17
β-strand	467	1	4
α-helix	470-483	14
α-helix	487-490	4
α-helix	492-511	20
α-helix	523-525	3
β-strand	526-532	7	6
α-helix	533-535	3
α-helix	549-552	4
α-helix	555-565	11
β-strand	570-573	4	6
β-strand	579-585	7	6
β-strand	590-596	7	6
α-helix	597-607	11
β-strand	614-615	2	7
α-helix	616-623	8
α-helix	627-638	12
β-strand	648-650	3	7
α-helix	657-659	3
β-strand	665-668	4	7
β-strand	675-676	2	8
β-strand	679-680	2	8
β-strand	685-687	3	6
α-helix	690-693	4
α-helix	698-725	28
β-strand	728-730	3	9
α-helix	731-741	11
α-helix	742-744	3
β-strand	746	1	5
α-helix	750-762	13
β-strand	767-769	3	9
β-strand	772-777	6	9

Chain C: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	6
α-helix	62-64	3
β-strand	75-76	2	10
β-strand	84-85	2	10
α-helix	89-92	4
β-strand	98	1	11
β-strand	105	1	11

Chain D: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	12
β-strand	10	1	13
β-strand	12-18	7	12
α-helix	24-35	12
β-strand	46	1	14
β-strand	49	1	14
β-strand	52	1	15
β-strand	54	1	15
α-helix	64-66	3
α-helix	72	1
β-strand	73-75	3	12
β-strand	90	1	13
α-helix	91-96	6

Chain E: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
α-helix	17-20	4
α-helix	24-28	5
β-strand	43-45	3	12
α-helix	51-66	16
α-helix	84-91	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein-L-isoaspartate O-methyltransferase domain-containing protein 1	A	protein	358	Homo sapiens	Q96MG8 (AlphaFold model)
Cullin-5	B	protein	783	Homo sapiens	Q93034 (AlphaFold model)
RING-box protein 2	C	protein	113	Mus musculus	Q9WTZ1 (AlphaFold model)
Elongin-B	D	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	E	protein	96	Homo sapiens	Q15369

Sequence of entity 1 (A), FASTA

>9OMF_1 Protein-L-isoaspartate O-methyltransferase domain-containing protein 1 (chains A)
SMGGAVSAGEDNDDLIDNLKEAQYIRTERVEQAFRAIDRGDYYLEGYRDNAYKDLAWKHG
NIHLSAPCIYSEVMEALKLQPGLSFLNLGSGTGYLSTMVGLILGPFGINHGIELHSDVVE
YAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLQIASDSHQYDRIYCGAGVQKDHENYMKI
LLKVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLVQPSKNDNGKPDSVGLPPCA
VRNLQDLARIYIRRTLRNFINDEMQAKGIPQRAPPKRKRKRVKQRINTYVFVGNQLIPQP
LDSEEDEKMEEDIKEEEEKDHNEAMKPEEPPQNLLREKIMKLPLPESLKAYLTYFRDK

Sequence of entity 2 (B), FASTA

>9OMF_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

>9OMF_3 RING-box protein 2 (chains C)
MADVEDGEEPCVLSSHSGSAGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDA
CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK

Sequence of entity 4 (D), FASTA

>9OMF_4 Elongin-B (chains D)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 5 (E), FASTA

>9OMF_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:

9OMA 4.14 Å, Cryo-EM structure of PCMTD1-ELOBC-CUL5-RBX2 (CRL5-PCMTD1)

Browse structure collections

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