3ZKE: LC8

Structure of LC8 in complex with Nek9 peptide. Determined by X-ray diffraction at 2.2 Å resolution. Released 20 Mar 2013.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: HOMO SAPIENS
Chains: 12
Atoms: 4,726
Mol. weight: 69 kDa
Released: 20 Mar 2013

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

Secondary structure: helices and β-sheets

3ZKE contains 12 α-helices and 30 β-strands across 12 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 K: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	15-31	17
α-helix	35-50	16
β-strand	54-69	16	1
β-strand	73-78	6	1
β-strand	81-87	7	1

Chains B, D, F, H, J and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	942-948	7	1

Chains C, E, G and I: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	15-31	17
α-helix	35-50	16
β-strand	54-69	16	1
β-strand	72-78	7	1
β-strand	81-87	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dynein light chain 1, cytoplasmic	A, C, E, G, I, K	protein	89	HOMO SAPIENS	P63167 (AlphaFold model)
NEK9 protein	B, D, F, H, J, L	protein	11	HOMO SAPIENS	Q8TD19 (AlphaFold model)

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

>3ZKE_1 DYNEIN LIGHT CHAIN 1, CYTOPLASMIC (chains A, C, E, G, I, K)
MCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGR
NFGSYVTHETKHFIYFYLGQVAILLFKSG

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

>3ZKE_2 NEK9 PROTEIN (chains B, D, F, H, J, L)
VGMHSKGTQTA

Primary citation

Structural Analysis of the Regulation of the Dynll/Lc8 Binding to Nek9 by Phosphorylation. Gallego, P., Velazquez-Campoy, A., Regue, L. et al. J Biol Chem (2013) 288:12283. DOI 10.1074/JBC.M113.459149 · PubMed

Other PDB entries of the same protein (UniProt P63167 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9NZ7 1.41 Å, Crystal structure of human DYNLL1-S64A/S88A mutant dimer
6GZL 1.95 Å, Complex between the dynein light chain DYNLL1/DLC8 and a peptide from the large…
6GZJ 1.98 Å, Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large…
7D35 2.4 Å, Human LC8 bound to ebola virus VP35(67-76)
1CMI 2.5 Å, Structure of the human PIN/LC8 dimer with a bound peptide
3ZKF 2.6 Å, Structure of LC8 in complex with Nek9 phosphopeptide
9BLY 3.5 Å, Composite structure of full-length human dynein-1 in phi-particle conformation
6SC2 3.9 Å, Structure of the dynein-2 complex; IFT-train bound model
8RGG 4.0 Å, Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy…
9E28 4.4 Å, Cryo-EM structure of Phi dynein tail
6RLB 4.5 Å, Structure of the dynein-2 complex; tail domain
9E12 4.5 Å, Full-length human dynein-1 in phi comformation under Lis1 condition

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