9N1F: Ark2C-Ubc13~Ub-Mms2 complex

Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,541
Mol. weight: 52.5 kDa
Ligands: ZN
Released: 11 Jun 2025

Explore 9N1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N1F contains 22 α-helices and 30 β-strands across 4 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	257-264	8
β-strand	266-269	4	1
β-strand	293	1	2
α-helix	299	1
β-strand	300	1	2
α-helix	301	1
β-strand	306-309	4	1
β-strand	315-317	3	1
α-helix	318-327	10
β-strand	330	1	3
β-strand	337	1	3

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	4
β-strand	31-40	10	4
α-helix	41-42	2
β-strand	51-57	7	4
α-helix	66-67	2
β-strand	68-71	4	4
β-strand	77	1	5
β-strand	80	1	5
β-strand	86	1	5
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
β-strand	31-35	5	6
β-strand	45-51	7	6
α-helix	52-53	2
β-strand	62-68	7	6
α-helix	77-78	2
β-strand	79-82	4	6
β-strand	84	1	7
β-strand	91	1	8
β-strand	97	1	6
β-strand	98	1	8
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	137-138	2
β-strand	142	1	7

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
β-strand	55	1	10
α-helix	56-59	4
β-strand	66-71	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase ARK2C	A	protein	87	Homo sapiens	Q6ZSG1 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	157	Homo sapiens	P61088 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 variant 2	C	protein	145	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9N1F_1 E3 ubiquitin-protein ligase ARK2C (chains A)
GPLGSGAVQNTIERFTFPHKYKKDEGEESDTDEKCTICLSMLEDGEDVRRLPCMHLFHQL
CVDQWLAMSKKCPICRVDIETQLGADS

Sequence of entity 2 (B), FASTA

>9N1F_2 Ubiquitin-conjugating enzyme E2 N (chains B)
GPLGSMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLE
LFLPEEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILTDQWSPALQIRTVLLSIQALLSAP
NPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C), FASTA

>9N1F_3 Ubiquitin-conjugating enzyme E2 variant 2 (chains C)
MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVAWGLEDDEDMTLTRWTGMIIGPPRTNYEN
RIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQ
ELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 4 (D), FASTA

>9N1F_4 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Arkadia and Ark2C Promote Substrate Ubiquitylation with Multiple E2 Enzymes. Rossig, C., Paluda, A., Chen, R. et al. J Mol Biol (2025) 437:169259-169259. DOI 10.1016/j.jmb.2025.169259 · PubMed

Other PDB entries of the same protein (UniProt Q6ZSG1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5D0I 1.9 Å, Structure of RING finger protein 165
5D0M 1.91 Å, Structure of UbE2D2:RNF165:Ub complex
5ULH 1.95 Å, Structure of RNF165 in complex with a UbcH5b~Ub conjugate
5ULK 2.38 Å, Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate
7R70 2.5 Å, Crystal Structure of the UbArk2C fusion protein
5D0K 2.65 Å, Structure of UbE2D2:RNF165:Ub complex
7R71 2.8 Å, Crystal Structure of the UbArk2C-UbcH5b~Ub complex
9QAL Solution NMR structure of Arkadia 2 RING domain

Browse structure collections

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