9AVW: TAB2 NZF domain

Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin. Determined by X-ray diffraction at 1.75 Å resolution. Released 31 Jul 2024.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,560
Mol. weight: 38.7 kDa
Ligands: ZN
Released: 31 Jul 2024

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

Secondary structure: helices and β-sheets

9AVW contains 8 α-helices and 18 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.

Chains A and B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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
α-helix	57-59	3
β-strand	66-71	6	1

Chain C: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	668-669	2	5
β-strand	676-677	2	5
β-strand	683	1	6
β-strand	690	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	152	Homo sapiens	P0CG47 (AlphaFold model)
TGF-beta-activated kinase 1 and MAP3K7-binding protein 2	C	protein	31	Homo sapiens	Q9NYJ8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9AVW_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Sequence of entity 2 (C), FASTA

>9AVW_2 TGF-beta-activated kinase 1 and MAP3K7-binding protein 2 (chains C)
DEGAQWNCTACTFLNHPALIRCEQCEMPRHF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin. Michel, M.A., Scutts, S., Komander, D. To be published.

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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