4C95: Carboxy-terminal domain of yeast Ctf4

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Sld5. Determined by X-ray diffraction at 2.69 Å resolution. Released 30 Apr 2014.

Method: X-ray diffraction
Resolution: 2.69 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 5
Atoms: 9,684
Mol. weight: 167.58 kDa
Released: 30 Apr 2014

Explore 4C95 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C95 contains 36 α-helices and 75 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, 25 β-strands

Element	Residues	Length	Sheet
α-helix	475-478	4
β-strand	479	1	1
β-strand	491-496	6	2
β-strand	500-507	8	2
β-strand	510-517	8	2
β-strand	526-530	5	2
β-strand	536-539	4	3
β-strand	543-547	5	3
β-strand	553-558	6	3
α-helix	564-565	2
β-strand	566-569	4	3
β-strand	578-583	6	1
β-strand	588-592	5	1
β-strand	596-600	5	1
β-strand	606-611	6	1
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
β-strand	777	1	5
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, 26 β-strands

Element	Residues	Length	Sheet
α-helix	475-478	4
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	667-669	3
α-helix	674-679	6
β-strand	686-689	4	1
β-strand	695-698	4	1
β-strand	703-708	6	1
β-strand	717-723	7	1
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
β-strand	777	1	1
α-helix	783-788	6
α-helix	819-841	23
α-helix	851-875	25
α-helix	879-887	9
α-helix	892-904	13
α-helix	908-925	18

Chain C: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	477-478	2
β-strand	479	1	5
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	740-748	9	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	6-14	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase alpha-binding protein	A, B, C	protein	478	SACCHAROMYCES CEREVISIAE	Q01454 (AlphaFold model)
DNA replication complex gins protein SLD5	D, E	protein	19	SACCHAROMYCES CEREVISIAE	Q03406 (AlphaFold model)

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

>4C95_1 DNA POLYMERASE ALPHA-BINDING PROTEIN (chains A, B, C)
MGSSHHHHHHSQDPENLYFQGTGKFRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSE
QYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKI
IPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVH
YSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFF
SSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAY
DTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEG
EEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRL
FASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQLK

Sequence of entity 2 (D, E), FASTA

>4C95_2 DNA REPLICATION COMPLEX GINS PROTEIN SLD5 (chains D, E)
MDINIDDILAELDKETTAV

Primary citation

A Ctf4 Trimer Couples the Cmg Helicase to DNA Polymerase a in the Eukaryotic Replisome. Simon, A.C., Zhou, J.C., Perera, R.L. et al. Nature (2014) 510:293. DOI 10.1038/NATURE13234 · 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.
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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