3OJ4: A20 ZnF4, ubiquitin and UbcH5A complex

Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex. Determined by X-ray diffraction at 3.4 Å resolution. Released 8 Dec 2010.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,988
Mol. weight: 63.24 kDa
Ligands: ZN
Released: 8 Dec 2010

Explore 3OJ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OJ4 contains 24 α-helices and 34 β-strands across 6 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.

Chains A and D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
β-strand	21-26	6	1
β-strand	29-38	10	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chains B and E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-33	11
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
β-strand	55	1	4
α-helix	56-59	4
β-strand	66-71	6	3

Chains C and F: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	606	1	5
β-strand	615	1	5
α-helix	618-620	3
α-helix	625-634	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D1	A, D	protein	153	Homo sapiens	P51668 (AlphaFold model)
Ubiquitin	B, E	protein	79	Homo sapiens	P0CG48 (AlphaFold model)
Tumor necrosis factor alpha-induced protein 3	C, F	protein	49	Homo sapiens	P21580 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3OJ4_1 Ubiquitin-conjugating enzyme E2 D1 (chains A, D)
GSHMLEMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTV
HFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPN
PDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 2 (B, E), FASTA

>3OJ4_2 Ubiquitin (chains B, E)
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Sequence of entity 3 (C, F), FASTA

>3OJ4_3 Tumor necrosis factor alpha-induced protein 3 (chains C, F)
GSPEFSQAARTPGDRTGTSKCRKAGCVYFGTPENKGFCTLCFIEYRENK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB Signaling. Bosanac, I., Wertz, I.E., Pan, B. et al. Mol Cell (2010) 40:548-557. DOI 10.1016/j.molcel.2010.10.009 · PubMed

Other PDB entries of the same protein (UniProt P51668 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4QPL 1.9 Å, Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex
2YHO 2.1 Å, The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
6D4P 2.11 Å, Ube2D1 in complex with ubiquitin variant Ubv.D1.1
4AP4 2.21 Å, Rnf4 - ubch5a - ubiquitin heterotrimeric complex
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
2C4P 2.35 Å, Crystal structure of human ubiquitin-conjugating enzyme UbcH5A
7ZJ3 2.53 Å, Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate
5TUT 2.6 Å, UbcH5a-Ub isopeptide conjugate
3PTF 2.7 Å, X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin
9V09 3.25 Å, Cryo-EM structure of lenalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9V0C 3.27 Å, Cryo-EM structure of iberdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9UUM 3.41 Å, Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…

Browse structure collections

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