9PEO: Replication factor C subunit 1

Name: PDB 9PEO: Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed nucleotide occupancy
Published: 2025-11-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: replication

Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed nucleotide occupancy. Determined by electron microscopy at 2.57 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.57 Å
Organism: Saccharomyces cerevisiae
Chains: 5
Atoms: 12,323
Mol. weight: 250.28 kDa
Ligands: GDP, ADP
Released: 12 Nov 2025

Explore 9PEO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PEO contains 113 α-helices and 33 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: 24 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	545-558	14
β-strand	560	1	1
α-helix	562-564	3
α-helix	566-571	6
α-helix	574-582	9
α-helix	588-595	8
β-strand	599-601	3	1
α-helix	604-605	2
α-helix	610-632	23
α-helix	638-640	3
α-helix	641-645	5
α-helix	646-650	5
α-helix	651-655	5
β-strand	658-660	3	1
α-helix	665-667	3
α-helix	669-690	22
α-helix	698-700	3
α-helix	701-705	5
α-helix	706-713	8
α-helix	715-720	6
α-helix	721-724	4
α-helix	725-733	9
α-helix	739-745	7
α-helix	746-748	3
α-helix	751-753	3
α-helix	756-761	6
α-helix	764-775	12

Chain B: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	20-22	3
α-helix	27-39	13
α-helix	42-44	3
β-strand	45-49	5	2
α-helix	55-66	12
α-helix	68-70	3
α-helix	71-74	4
β-strand	75-79	5	2
α-helix	86-97	12
β-strand	109-114	6	2
α-helix	116-118	3
α-helix	121-133	13
β-strand	138-144	7	2
α-helix	152-157	6
β-strand	159-163	5	2
α-helix	165-167	3
α-helix	168-182	15
β-strand	186	1	3
α-helix	188-197	10
α-helix	202-216	15
β-strand	219	1	3
α-helix	221-227	7
α-helix	231-232	2
α-helix	233-241	9
α-helix	245-251	7
α-helix	252-257	6
α-helix	263-275	13
α-helix	282-300	19
α-helix	306-321	16

Chain C: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	31-43	13
β-strand	49-52	4	4
α-helix	59-70	12
α-helix	75-78	4
β-strand	79-83	5	4
α-helix	84-86	3
α-helix	90-102	13
β-strand	112-117	6	4
α-helix	119-121	3
α-helix	124-136	13
β-strand	141-147	7	4
α-helix	150-152	3
α-helix	155-159	5
β-strand	162-165	4	4
α-helix	166-170	5
α-helix	171-185	15
β-strand	188-189	2	5
α-helix	191-201	11
α-helix	205-218	14
β-strand	226-227	2	5
α-helix	228	1
α-helix	229-236	8
α-helix	241-253	13
α-helix	256-269	14
α-helix	274-286	13
α-helix	293-311	19
α-helix	316-330	15
α-helix	331-333	3

Chain D: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	36-38	3
α-helix	43-54	12
β-strand	60-64	5	6
α-helix	71-82	12
α-helix	87-89	3
β-strand	92-96	5	6
α-helix	103-115	13
α-helix	117-121	5
α-helix	123-128	6
β-strand	135-140	6	6
α-helix	142-144	3
α-helix	147-159	13
β-strand	164-170	7	6
α-helix	173-175	3
α-helix	178-182	5
β-strand	184-188	5	6
α-helix	189-193	5
α-helix	194-207	14
β-strand	212	1	7
α-helix	216-224	9
α-helix	228-244	17
α-helix	249-250	2
β-strand	251	1	7
α-helix	253-260	8
α-helix	265-277	13
α-helix	280-291	12
α-helix	297-309	13
α-helix	316-333	18
α-helix	339-351	13

Chain E: 22 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	13-15	3
α-helix	20-30	11
α-helix	36-38	3
β-strand	39-42	4	8
α-helix	49-60	12
α-helix	63-66	4
β-strand	69-76	8	8
α-helix	78-80	3
β-strand	82-89	8	8
β-strand	93-96	4	8
α-helix	98-104	7
α-helix	105-119	15
β-strand	136-141	6	8
α-helix	143-145	3
α-helix	148-160	13
β-strand	165-171	7	8
α-helix	179-184	6
β-strand	186-189	4	8
α-helix	191-194	4
α-helix	195-209	15
β-strand	212-213	2	9
α-helix	217-226	10
α-helix	230-243	14
β-strand	247-248	2	9
α-helix	252-255	4
α-helix	258-272	15
α-helix	276-291	16
α-helix	296-307	12
α-helix	315-333	19
α-helix	338-353	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replication factor C subunit 1	A	protein	861	Saccharomyces cerevisiae	P38630 (AlphaFold model)
Replication factor C subunit 4	B	protein	323	Saccharomyces cerevisiae	P40339 (AlphaFold model)
Replication factor C subunit 3	C	protein	340	Saccharomyces cerevisiae	P38629 (AlphaFold model)
Replication factor C subunit 2	D	protein	353	Saccharomyces cerevisiae	P40348 (AlphaFold model)
Replication factor C subunit 5	E	protein	354	Saccharomyces cerevisiae	P38251

Sequence of entity 1 (A), FASTA

>9PEO_1 Replication factor C subunit 1 (chains A)
MVNISDFFGKNKKSVRSSTSRPTRQVGSSKPEVIDLDTESDQESTNKTPKKMPVSNVIDV
SETPEGEKKLPLPAKRKASSPTVKPASSKKTKPSSKSSDSASNITAQDVLDKIPSLDLSN
VHVKENAKFDFKSANSNADPDEIVSEIGSFPEGKPNCLLGLTIVFTGVLPTLERGASEAL
AKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLIAGMPAEGGDG
EAAEKARRKLEEQHNIATKEAELLVKKEEERSKKLAATRVSGGHLERDNVVREEDKLWTV
KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKT
TAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFV
IIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDA
NSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEIS
KAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLMIQENYLSTR
PSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLHAVLSSVYPASKVAGHM
AGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIGLRLDYLPTFRKRLLDPFLKQ
GADAISSVIEVMDDYYLTKEDWDSIMEFFVGPDVTTAIIKKIPATVKSGFTRKYNSMTHP
VAIYRTGSTIGGGGVGTSTSTPDFEDVVDADDNPVPADDEETQDSSTDLKKDKLIKQKAK
PTKRKTATSKPGGSKKRKTKA

Sequence of entity 2 (B), FASTA

>9PEO_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>9PEO_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>9PEO_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>9PEO_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (ACT) are not listed.

Primary citation

PCNA is a nucleotide exchange factor for the clamp loader ATPase complex. Pajak, J., Landeck, J.T., Liu, X. et al. Proc Natl Acad Sci U S A (2025) 122:e2518834122-e2518834122. DOI 10.1073/pnas.2518834122 · PubMed

Other PDB entries of the same protein (UniProt P38630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8DQX 2.1 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR1 2.14 Å, Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
8DR3 2.2 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
8DR6 2.39 Å, Closed state of RFC:PCNA bound to a nicked dsDNA
8DR0 2.42 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
8DR4 2.45 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
9PER 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PET 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PES 2.59 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PEU 2.62 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
9PEV 2.63 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
8DR7 2.7 Å, Open state of RFC:PCNA bound to a nicked dsDNA

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