4XKL: NDP52 ZF2

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin. Determined by X-ray diffraction at 2.1 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,894
Mol. weight: 26.08 kDa
Ligands: ZN
Released: 11 Nov 2015

Explore 4XKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XKL contains 12 α-helices and 18 β-strands across 4 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: 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

Chains B and D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	419-421	3	3
β-strand	428-430	3	3
α-helix	434-443	10

Chain C: 6 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	41-44	4	4
β-strand	49	1	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	66-71	6	4
α-helix	73	1
α-helix	75	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, C	protein	80	Homo sapiens	P62987 (AlphaFold model)
Calcium-binding and coiled-coil domain-containing protein 2	B, D	protein	33	Homo sapiens	Q13137 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4XKL_1 Ubiquitin (chains A, C)
GPGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGG

Sequence of entity 2 (B, D), FASTA

>4XKL_2 Calcium-binding and coiled-coil domain-containing protein 2 (chains B, D)
QMQPLCFNCPICDKIFPATEKQIFEDHVFCHSL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

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

Primary citation

Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. Xie, X., Li, F., Wang, Y. et al. Autophagy (2015) 11:1775-1789. DOI 10.1080/15548627.2015.1082025 · PubMed

Other PDB entries of the same protein (UniProt P62987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
4PIH 1.5 Å, X-ray crystal structure of the K33S mutant of ubiquitin
4PIJ 1.5 Å, X-ray crystal structure of the K11S/K63S double mutant of ubiquitin
5GOJ 1.55 Å, Lys63-linked di-ubiquitin
5J8P 1.55 Å, Lys27-linked diubiquitin
5GOI 1.59 Å, Lys48-linked di-ubiquitin
8A3D 1.67 Å, Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound
5GOC 1.73 Å, Lys11-linked diubiquitin
29IW 1.77 Å, Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.
8QYX 1.78 Å, Human 60S ribosomal subunit
4HJK 1.78 Å, U7Ub7 Disulfide variant

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