5NXQ: Carboxy-terminal domain of yeast Ctf4

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP. Determined by X-ray diffraction at 2.41 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 9,931
Mol. weight: 168.32 kDa
Released: 30 Aug 2017

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

Secondary structure: helices and β-sheets

5NXQ contains 36 α-helices and 71 β-strands across 5 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: 13 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	476-478	3
β-strand	491-496	6	1
β-strand	500-507	8	1
β-strand	510-517	8	1
β-strand	526-530	5	1
β-strand	536-539	4	2
β-strand	543-547	5	2
β-strand	553-558	6	2
α-helix	564-565	2
β-strand	566-569	4	2
β-strand	578-583	6	3
β-strand	588-592	5	3
β-strand	596-600	5	3
β-strand	606-611	6	3
α-helix	614	1
β-strand	615-621	7	4
β-strand	624-631	8	4
β-strand	635-643	9	4
β-strand	648-656	9	4
α-helix	659-662	4
α-helix	674-679	6
β-strand	686-689	4	5
β-strand	695-698	4	5
β-strand	703-708	6	5
β-strand	717-723	7	5
α-helix	724-731	8
β-strand	740-748	9	6
β-strand	751-758	8	6
α-helix	768-771	4
β-strand	772-775	4	6
α-helix	783-788	6
α-helix	819-843	25
α-helix	851-875	25
α-helix	879-887	9
α-helix	892-904	13
α-helix	908-925	18

Chain B: 14 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	476-478	3
β-strand	479	1	7
β-strand	491-496	6	8
β-strand	500-507	8	8
β-strand	510-517	8	8
β-strand	526-530	5	8
β-strand	536-539	4	9
β-strand	543-547	5	9
β-strand	553-558	6	9
α-helix	564-565	2
β-strand	566-569	4	9
β-strand	578-583	6	7
β-strand	587-592	6	7
β-strand	596-601	6	7
β-strand	606	1	7
β-strand	610-611	2	7
α-helix	614	1
β-strand	615-621	7	10
β-strand	624-631	8	10
β-strand	635-643	9	10
β-strand	648-656	9	10
α-helix	659-662	4
α-helix	667-670	4
α-helix	674-679	6
β-strand	686-689	4	3
β-strand	695-698	4	3
β-strand	703-708	6	3
β-strand	717-723	7	3
α-helix	724-731	8
β-strand	740-748	9	11
β-strand	751-758	8	11
α-helix	768-771	4
β-strand	772-775	4	11
α-helix	783-788	6
α-helix	819-843	25
α-helix	851-875	25
α-helix	879-887	9
α-helix	892-904	13
α-helix	908-925	18

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	476-478	3
β-strand	491-496	6	12
β-strand	500-506	7	12
β-strand	511-517	7	12
β-strand	526-530	5	12
β-strand	536-539	4	13
β-strand	543-547	5	13
β-strand	553-558	6	13
α-helix	564-565	2
β-strand	566-569	4	13
β-strand	578-583	6	5
β-strand	588-592	5	5
β-strand	596-600	5	5
β-strand	606-611	6	5
α-helix	614	1
β-strand	615-621	7	14
β-strand	624-631	8	14
β-strand	635-643	9	14
β-strand	648-656	9	14
α-helix	659-662	4
α-helix	674-679	6
β-strand	686-689	4	15
β-strand	695-698	4	15
β-strand	703-708	6	15
β-strand	717-723	7	15
α-helix	724-731	8
β-strand	740-747	8	16
β-strand	751-758	8	16
α-helix	768-771	4
β-strand	772-775	4	16

Chains D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha-binding protein	A, B, C	protein	479	Saccharomyces cerevisiae	Q01454 (AlphaFold model)
Met-asp-ile-UA1-ile-asp-asp-ile-leu-UA2-glu-leu-asp-lys-glu	D, E	protein	19	Saccharomyces cerevisiae	Q03406 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>5NXQ_1 DNA polymerase alpha-binding protein (chains A, B, C)
MGSSHHHHHHSQDPENLYFQGSTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNS
EQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTK
IIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSV
HYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLF
FSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALA
YDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEE
GEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLR
LFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

Sequence of entity 2 (D, E), FASTA

>5NXQ_2 MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU (chains D, E)
MDIXIDDILXELDKETTAV

Primary citation

Targeting the Genome-Stability Hub Ctf4 by Stapled-Peptide Design. Wu, Y., Villa, F., Maman, J. et al. Angew Chem Int Ed Engl (2017) 56:12866-12872. DOI 10.1002/anie.201705611 · PubMed

Other PDB entries of the same protein (UniProt Q01454 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4C8H 2.69 Å, Crystal structure of the C-terminal region of yeast Ctf4, selenomethionine protein.
4C93 2.69 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Pol alpha.
4C95 2.69 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Sld5
4C8S 3.0 Å, Crystal structure of the C-terminal region of yeast Ctf4
8KG6 3.07 Å, Yeast replisome in state I
5HOG 3.09 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.
7PMK 3.2 Å, S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I)
7PMN 3.2 Å, S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II)
5HOI 3.3 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2.
8B9A 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork…
8B9B 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA…
6SKL 3.7 Å, Cryo-EM structure of the CMG Fork Protection Complex at a replication fork -…

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