5YT6: TAX1BP1 UBZ2

Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin. Determined by X-ray diffraction at 1.5 Å resolution. Released 11 Jul 2018.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 8
Atoms: 3,900
Mol. weight: 52.52 kDa
Ligands: ZN
Released: 11 Jul 2018

Explore 5YT6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YT6 contains 23 α-helices and 36 β-strands across 8 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	4
β-strand	12-17	6	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
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	4

Chains B and F: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	35-36	2	6
β-strand	43-44	2	6
α-helix	50-59	10

Chains C and G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	7
β-strand	12-17	6	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7
α-helix	72-73	2

Chains D and H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	35-36	2	9
β-strand	43-44	2	9
α-helix	50-58	9

Chain E: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
β-strand	12-17	6	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
α-helix	57-59	3
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, C, E, G	protein	78	Homo sapiens	P0CG47 (AlphaFold model)
Tax1-binding protein 1	B, D, F, H	protein	35	Homo sapiens	Q86VP1 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5YT6_1 Ubiquitin (chains A, C, E, G)
GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG

Sequence of entity 2 (B, D, F, H), FASTA

>5YT6_2 Tax1-binding protein 1 (chains B, D, F, H)
SWKVCPMCSEQFPPDYDQQVFERHVQTHFDQNVLN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (SO4, GOL, EDO) are not listed.

Primary citation

Mechanistic Insights into Recognitions of Ubiquitin and Myosin VI by Autophagy Receptor TAX1BP1. Hu, S., Wang, Y., Gong, Y. et al. J Mol Biol (2018) 430:3283-3296. DOI 10.1016/j.jmb.2018.06.030 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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