5Z7L: NDP52 SKICH region

Crystal structure of NDP52 SKICH region in complex with NAP1. Determined by X-ray diffraction at 2.02 Å resolution. Released 2 Jan 2019.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,882
Mol. weight: 38.52 kDa
Released: 2 Jan 2019

Explore 5Z7L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z7L contains 13 α-helices and 20 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: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	23-26	4	1
β-strand	31	1	2
β-strand	38-44	7	1
β-strand	55-60	6	3
α-helix	66-68	3
β-strand	71-74	4	3
α-helix	75-78	4
α-helix	84-86	3
β-strand	89-93	5	1
α-helix	95-97	3
β-strand	105-110	6	3
β-strand	116-119	4	3
α-helix	120-122	3
β-strand	123	1	3
β-strand	124	1	2

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
β-strand	23-26	4	4
β-strand	31-32	2	5
β-strand	38-44	7	4
β-strand	55-60	6	6
α-helix	66-68	3
β-strand	71-74	4	6
α-helix	75-78	4
β-strand	88-93	6	4
α-helix	95-97	3
β-strand	105-110	6	6
β-strand	116-119	4	6
α-helix	120-122	3
β-strand	123	1	6
β-strand	124-125	2	5

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	34-72	39

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	36-73	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium-binding and coiled-coil domain-containing protein 2	A, B	protein	117	Homo sapiens	Q13137 (AlphaFold model)
5-azacytidine-induced protein 2	C, D	protein	43	Homo sapiens	Q9H6S1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5Z7L_1 Calcium-binding and coiled-coil domain-containing protein 2 (chains A, B)
TSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREY
YTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFR

Sequence of entity 2 (C, D), FASTA

>5Z7L_2 5-azacytidine-induced protein 2 (chains C, D)
ESVASHFALVTAYEDIKKRLKDSEKENSLLKKRIRFLEEKLIA

Primary citation

Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1. Fu, T., Liu, J., Wang, Y. et al. Proc Natl Acad Sci U S A (2018) 115:E11651-E11660. DOI 10.1073/pnas.1811421115 · PubMed

Other PDB entries of the same protein (UniProt Q13137 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VVV 1.35 Å, Skich domain of NDP52
4GXL 2.02 Å, The crystal structure of Galectin-8 C-CRD in complex with NDP52
4XKL 2.1 Å, Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin
5Z7A 2.38 Å, Crystal structure of NDP52 SKICH region
3VVW 2.5 Å, NDP52 in complex with LC3C
4HAN 2.55 Å, Crystal structure of Galectin 8 with NDP52 peptide
7EAA 2.6 Å, crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain
2MXP Solution structure of NDP52 ubiquitin-binding zinc finger
5AAQ TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy

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