5HOI: Carboxy-terminal domain of yeast Ctf4

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2. Determined by X-ray diffraction at 3.3 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Saccharomyces cerevisiae
Chains: 6
Atoms: 9,650
Mol. weight: 170.89 kDa
Released: 22 Jun 2016

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

Secondary structure: helices and β-sheets

5HOI contains 37 α-helices and 70 β-strands across 6 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: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
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	624-630	7	4
β-strand	636-643	8	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
α-helix	713-715	3
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	783-790	8
α-helix	815-818	4
α-helix	819-843	25
α-helix	851-875	25
α-helix	879-887	9
α-helix	892-904	13
α-helix	908-924	17

Chain B: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
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	606-611	6	7
α-helix	614	1
β-strand	615-621	7	10
β-strand	624-630	7	10
β-strand	636-643	8	10
β-strand	648-656	9	10
α-helix	659-662	4
α-helix	667-669	3
α-helix	674-679	6
β-strand	686-689	4	11
β-strand	695-698	4	11
β-strand	703-708	6	11
α-helix	713-715	3
β-strand	717-723	7	11
α-helix	724-731	8
β-strand	740-748	9	12
β-strand	751-758	8	12
α-helix	768-771	4
β-strand	772-775	4	12
α-helix	783-790	8
α-helix	815-818	4
α-helix	819-843	25
α-helix	851-875	25
α-helix	879-887	9
α-helix	892-904	13
α-helix	908-926	19

Chain C: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	491-496	6	13
β-strand	500-506	7	13
β-strand	511-517	7	13
β-strand	526-530	5	13
β-strand	536-539	4	14
β-strand	543-547	5	14
β-strand	553-558	6	14
α-helix	564-565	2
β-strand	566-569	4	14
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	15
β-strand	624-631	8	15
β-strand	635-642	8	15
β-strand	649-656	8	15
α-helix	659-662	4
α-helix	674-679	6
β-strand	686-689	4	16
β-strand	695-698	4	16
β-strand	703-708	6	16
β-strand	717-723	7	16
α-helix	724-731	8
β-strand	740-748	9	17
β-strand	751-758	8	17
β-strand	772-775	4	17

Chains D and E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	503-512	10

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	505-510	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha-binding protein	A, B, C	protein	478	Saccharomyces cerevisiae	Q01454 (AlphaFold model)
Topoisomerase 1-associated factor 2	D, E, F	protein	21	Saccharomyces cerevisiae	Q02208 (AlphaFold model)

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

>5HOI_1 DNA polymerase alpha-binding protein (chains A, B, C)
MGSSHHHHHHSQDPENLYFQGTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSE
QYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKI
IPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVH
YSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFF
SSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAY
DTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEG
EEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRL
FASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

Sequence of entity 2 (D, E, F), FASTA

>5HOI_2 Topoisomerase 1-associated factor 2 (chains D, E, F)
SHAKDVKIQETIRKLNRFKPT

Primary citation

Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Villa, F., Simon, A.C., Ortiz Bazan, M.A. et al. Mol Cell (2016) 63:385-396. DOI 10.1016/j.molcel.2016.06.009 · PubMed

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

5NXQ 2.41 Å, Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP
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)
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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