3VVW: NDP52

NDP52 in complex with LC3C. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Feb 2013.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,902
Mol. weight: 29.41 kDa
Released: 27 Feb 2013

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

Secondary structure: helices and β-sheets

3VVW contains 8 α-helices and 20 β-strands across 2 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, 11 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	31-32	2	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	75-76	2
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	124-125	2	2
β-strand	133-135	3	4

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-32	14
β-strand	37-43	7	4
α-helix	51-52	2
β-strand	53	1	5
β-strand	57-60	4	4
β-strand	65	1	6
α-helix	66-75	10
β-strand	77	1	5
β-strand	86-89	4	4
β-strand	93	1	4
β-strand	100	1	6
α-helix	101-108	8
β-strand	115-120	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium-binding and coiled-coil domain-containing protein 2	A	protein	123	Homo sapiens	Q13137 (AlphaFold model)
Microtubule-associated proteins 1A/1B light chain 3C	B	protein	128	Homo sapiens	Q9BXW4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VVW_1 Calcium-binding and coiled-coil domain-containing protein 2 (chains A)
GPSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFRVGWKTTREYYTFMWVTLP
IDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGASIPFQFRPENEEDILVVTT
QGE

Sequence of entity 2 (B), FASTA

>3VVW_2 Microtubule-associated proteins 1A/1B light chain 3C (chains B)
GPMPPPQKIPSVRPFKQRKSLAIRQEEVAGIRAKFPNKIPVVVERYPRETFLPPLDKTKF
LVPQELTMTQFLSIIRSRMVLRATEAFYLLVNNKSLVSMSATMAEIYRDYKDEDGFVYMT
YASQETFG

Primary citation

LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Muhlinen, N.V., Akutsu, M., Ravenhill, B.J. et al. Mol Cell (2012) 48:329-342. DOI 10.1016/j.molcel.2012.08.024 · 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
5Z7L 2.02 Å, Crystal structure of NDP52 SKICH region in complex with NAP1
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
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

Browse structure collections

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