3VUY: A20 ZF7

Crystal structure of A20 ZF7 in complex with linear tetraubiquitin. Determined by X-ray diffraction at 1.98 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 6
Atoms: 2,731
Mol. weight: 37.97 kDa
Ligands: ZN
Released: 13 Feb 2013

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

Secondary structure: helices and β-sheets

3VUY contains 21 α-helices and 27 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 B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	11	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
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

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
β-strand	66-71	6	4

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	761	1	3
β-strand	770	1	3
α-helix	771	1
α-helix	773-775	3
α-helix	780-788	9

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	761	1	9
β-strand	770	1	9
α-helix	771	1
α-helix	773-775	3
α-helix	780-789	10

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	760	1
β-strand	761	1	6
α-helix	762	1
β-strand	770	1	6
α-helix	771	1
α-helix	780-788	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-C	A, B, C	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Tumor necrosis factor alpha-induced protein 3	D, E, F	protein	35	Homo sapiens	P21580 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3VUY_1 Polyubiquitin-C (chains A, B, C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (D, E, F), FASTA

>3VUY_2 Tumor necrosis factor alpha-induced protein 3 (chains D, E, F)
GPPKQRCRAPACDHFGNAKCNGYCNECFQFKQMYG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Water and common crystallization additives (K) are not listed.

Primary citation

Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-kappaB regulation. Tokunaga, F., Nishimasu, H., Ishitani, R. et al. EMBO J (2012) 31:3856-3870. DOI 10.1038/emboj.2012.241 · 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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