7R71: UbArk2C-UbcH5b~Ub complex

Crystal Structure of the UbArk2C-UbcH5b~Ub complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 9 Mar 2022.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,980
Mol. weight: 46.26 kDa
Ligands: ZN
Released: 9 Mar 2022

Explore 7R71 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R71 contains 16 α-helices and 31 β-strands across 3 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	12-17	6	1
β-strand	22	1	2
α-helix	23-34	12
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
β-strand	66-71	6	1
α-helix	261-264	4
β-strand	266-269	4	3
β-strand	293	1	4
α-helix	299	1
β-strand	300	1	4
α-helix	301	1
β-strand	306-309	4	3
β-strand	315-317	3	3
α-helix	318-325	8
β-strand	330	1	5
β-strand	337	1	5

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	21-26	6	9
β-strand	29-38	10	9
α-helix	39-40	2
β-strand	49-55	7	9
α-helix	64-65	2
β-strand	66-69	4	9
β-strand	75	1	10
β-strand	78	1	10
β-strand	83	1	9
β-strand	84	1	10
β-strand	86	1	8
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	12-14	3	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-50	3	6
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-71	6	6
β-strand	75	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin,E3 ubiquitin-protein ligase RNF165	A	protein	183	Homo sapiens	P0CG48 (AlphaFold model), Q6ZSG1 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D2	C	protein	152	Homo sapiens	P62837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7R71_1 Ubiquitin,E3 ubiquitin-protein ligase RNF165 (chains A)
GPLGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGGGESGSGGSGSGAVQNTIERFTFPHKYKKRRPQDGKGKKD
EGEESDTDEKCTICLSMLEDGEDVRRLPCMHLFHQLCVDQWLAMSKKCPICRVDIETQLG
ADS

Sequence of entity 2 (D), FASTA

>7R71_2 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>7R71_3 Ubiquitin-conjugating enzyme E2 D2 (chains C)
GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIH
FPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNP
DDPLVPEIARIYKTDREKYNRIAREWTQKYAM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C. Paluda, A., Middleton, A.J., Rossig, C. et al. Nat Commun (2022) 13:1181-1181. DOI 10.1038/s41467-022-28782-y · PubMed

Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant

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