6MF6: Budding yeast Cdc5 polo-box domain

Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4 polo-interacting region. Determined by X-ray diffraction at 3.4 Å resolution. Released 19 Feb 2020.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 3,701
Mol. weight: 71.42 kDa
Released: 19 Feb 2020

Explore 6MF6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MF6 contains 16 α-helices and 30 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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	456-459	4
β-strand	462-463	2	1
α-helix	465-467	3
α-helix	471-497	27
α-helix	505-507	3
β-strand	514-518	5	2
β-strand	526-530	5	2
β-strand	535-538	4	2
β-strand	544-547	4	2
β-strand	553-557	5	2
β-strand	558-560	3	3
β-strand	564-566	3	3
β-strand	569-571	3	2
α-helix	577-593	17
β-strand	615-621	7	1
β-strand	624-629	6	1
β-strand	634-638	5	1
β-strand	643-647	5	1
β-strand	652-656	5	1
β-strand	662-666	5	1
α-helix	667-673	7
α-helix	680-682	3
α-helix	684-699	16

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	457	1
α-helix	459	1
β-strand	464	1	4
α-helix	471-497	27
β-strand	514-518	5	5
β-strand	527-530	4	5
β-strand	535-538	4	5
β-strand	544-547	4	5
β-strand	553-559	7	5
β-strand	565-571	7	5
α-helix	577-596	20
β-strand	615-620	6	4
β-strand	624-629	6	4
β-strand	634-638	5	4
β-strand	643-646	4	4
β-strand	652-657	6	4
β-strand	661-666	6	4
α-helix	667-673	7
α-helix	684-698	15

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	84-85	2
β-strand	89	1	3

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	85	1
β-strand	89-90	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell cycle serine/threonine-protein kinase CDC5/MSD2	A, B	protein	290	Saccharomyces cerevisiae	P32562 (AlphaFold model)
DDK kinase regulatory subunit DBF4	C, D	protein	21	Saccharomyces cerevisiae	P32325 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6MF6_1 Cell cycle serine/threonine-protein kinase CDC5/MSD2 (chains A, B)
GALSPGGTKQKYKEVVDIEAQRRLNDLAREARIRRAQQAVLRKELIATSTNVIKSEISLR
ILASECHLTLNGIVEAEAQYKMGGLPKSRLPKIKHPMIVTKWVDYSNKHGFSYQLSTEDI
GVLFNNGTTVLRLADAEEFWYISYDDREGWVASHYLLSEKPRELSRHLEVVDFFAKYMKA
NLSRVSTFGREEYHKDDVFLRRYTRYKPFVMFELSDGTFQFNFKDHHKMAISDGGKLVTY
ISPSHESTTYPLVEVLKYGEIPGYPESNFREKLTLIKEGLKQKSTIVTVD

Sequence of entity 2 (C, D), FASTA

>6MF6_2 DDK kinase regulatory subunit DBF4 (chains C, D)
RARIERARSIEGAVQVSKGTG

Primary citation

Distinct surfaces on Cdc5/PLK Polo-box domain orchestrate combinatorial substrate recognition during cell division. Almawi, A.W., Langlois-Lemay, L., Boulton, S. et al. Sci Rep (2020) 10:3379-3379. DOI 10.1038/s41598-020-60344-4 · PubMed

Other PDB entries of the same protein (UniProt P32562 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MF4 1.8 Å, Crystal structure of the polo-box domain of Cdc5 from budding yeast.
6MF5 2.7 Å, Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72…

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