7TFJ: Replication factor C subunit 1

Atomic model of S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with a closed clamp ring. Determined by electron microscopy at 3.3 Å resolution. Released 16 Nov 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Saccharomyces cerevisiae, synthetic construct
Chains: 10
Atoms: 20,607
Mol. weight: 358.41 kDa
Ligands: AGS, MG, ADP
Released: 16 Nov 2022

Explore 7TFJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TFJ contains 142 α-helices and 110 β-strands across 8 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: 30 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	298-301	4
α-helix	307-309	3
α-helix	314-325	12
α-helix	327-332	6
β-strand	348-352	5	1
α-helix	359-369	11
α-helix	372	1
β-strand	373-377	5	1
α-helix	385-389	5
α-helix	394-396	3
β-strand	398	1	2
α-helix	402-405	4
β-strand	419-423	5	1
α-helix	426-428	3
α-helix	437-445	9
β-strand	451-455	5	1
α-helix	464-466	3
β-strand	471	1	1
β-strand	474	1	1
α-helix	477-479	3
α-helix	480-493	14
β-strand	497-498	2	3
α-helix	502-510	9
α-helix	514-527	14
β-strand	530-531	2	3
α-helix	536-542	7
α-helix	547-550	4
α-helix	551-558	8
α-helix	566-571	6
α-helix	574-583	10
α-helix	588-594	7
β-strand	599	1	4
α-helix	604-605	2
α-helix	610-631	22
α-helix	638-640	3
α-helix	641-645	5
α-helix	646-650	5
α-helix	651-653	3
β-strand	660	1	4
α-helix	664-666	3
α-helix	669-690	22

Chain B: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-14	4
α-helix	27-39	13
α-helix	42-44	3
β-strand	45-48	4	5
α-helix	56-66	11
α-helix	71-74	4
β-strand	75-78	4	5
α-helix	86-88	3
α-helix	89-93	5
α-helix	94-98	5
β-strand	99	1	6
β-strand	109-114	6	5
α-helix	116-118	3
α-helix	121-133	13
β-strand	138-144	7	5
α-helix	152-157	6
β-strand	159-162	4	5
α-helix	165-167	3
α-helix	168-181	14
β-strand	185-186	2	7
α-helix	188-198	11
α-helix	202-215	14
β-strand	218-219	2	7
α-helix	221-227	7
α-helix	229-231	3
α-helix	232-241	10
α-helix	245-252	8
α-helix	253-257	5
α-helix	263-276	14
α-helix	282-301	20
α-helix	306-320	15

Chain C: 20 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	32-43	12
β-strand	49-52	4	8
α-helix	59-70	12
α-helix	75-78	4
β-strand	79-81	3	8
α-helix	90-92	3
α-helix	93-97	5
α-helix	98-102	5
β-strand	103	1	9
α-helix	104-105	2
β-strand	112-116	5	8
α-helix	124-136	13
β-strand	141-147	7	8
α-helix	155-160	6
β-strand	162-165	4	8
α-helix	167-169	3
α-helix	171-185	15
β-strand	188-189	2	10
α-helix	191-201	11
α-helix	205-218	14
β-strand	226-227	2	10
α-helix	229-236	8
α-helix	241-253	13
α-helix	256-270	15
α-helix	274-287	14
α-helix	293-311	19
α-helix	316-332	17

Chain D: 28 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	36-38	3
α-helix	43-54	12
α-helix	58-60	3
β-strand	61-64	4	11
α-helix	71-82	12
α-helix	88-91	4
β-strand	92-95	4	11
α-helix	103-105	3
α-helix	106-110	5
α-helix	111-115	5
α-helix	117-122	6
α-helix	123-128	6
β-strand	135-140	6	11
α-helix	142-144	3
α-helix	147-159	13
α-helix	160-162	3
β-strand	164-169	6	11
α-helix	178-183	6
β-strand	185-188	4	11
α-helix	190-192	3
α-helix	198-208	11
β-strand	212	1	12
α-helix	216-223	8
α-helix	228-245	18
α-helix	250	1
β-strand	251	1	12
α-helix	252	1
α-helix	253-259	7
α-helix	262-264	3
α-helix	265-276	12
α-helix	280-293	14
α-helix	297-308	12
α-helix	316-334	19
α-helix	339-352	14

Chain E: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	20-31	12
α-helix	37-38	2
β-strand	39-42	4	13
α-helix	49-60	12
β-strand	69-76	8	13
β-strand	82-90	9	13
β-strand	93-96	4	13
α-helix	106-118	13
β-strand	136-140	5	13
α-helix	143-145	3
α-helix	148-160	13
β-strand	165-170	6	13
α-helix	179-184	6
β-strand	186-189	4	13
α-helix	191-194	4
α-helix	195-208	14
α-helix	217-226	10
α-helix	230-243	14
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	340-352	13

Chain F: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
α-helix	10-18	9
β-strand	25-30	6	15
β-strand	34-40	7	15
β-strand	46-53	8	15
β-strand	57-62	6	14
β-strand	66-71	6	15
α-helix	72-79	8
β-strand	87-92	6	14
β-strand	98-104	7	14
β-strand	112-117	6	14
β-strand	119	1	15
β-strand	135-140	6	15
α-helix	141-152	12
β-strand	157-163	7	16
β-strand	166-170	5	16
β-strand	176	1	16
β-strand	179-182	4	16
β-strand	185	1	17
α-helix	191-193	3
β-strand	195	1	17
β-strand	196	1	15
β-strand	199	1	15
β-strand	203-208	6	16
α-helix	209-216	8
α-helix	217-220	4
β-strand	224-230	7	15
β-strand	233-240	8	15
β-strand	245-250	6	15
α-helix	251-252	2
β-strand	253	1	9
α-helix	254	1

Chain G: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	16
β-strand	5	1	16
α-helix	9-18	10
β-strand	25-30	6	18
β-strand	34-40	7	18
β-strand	46-53	8	18
β-strand	59	1	16
β-strand	62	1	16
β-strand	66-71	6	18
α-helix	72-79	8
β-strand	87-92	6	16
β-strand	98-104	7	16
β-strand	110-117	8	16
α-helix	118	1
β-strand	119	1	6
α-helix	124-126	3
β-strand	135-140	6	18
α-helix	141-152	12
β-strand	157-158	2	19
β-strand	159	1	20
β-strand	162	1	20
β-strand	167-172	6	20
β-strand	177-182	6	20
β-strand	185	1	21
α-helix	191-193	3
β-strand	195	1	21
β-strand	196-199	4	18
β-strand	207-208	2	19
α-helix	210-216	7
β-strand	224-230	7	18
β-strand	233-240	8	18
β-strand	244-250	7	18
β-strand	253	1	2

Chain H: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	20
α-helix	10-18	9
β-strand	25-31	7	22
β-strand	34-40	7	22
β-strand	46-53	8	22
β-strand	59	1	20
β-strand	62	1	20
β-strand	66-71	6	22
α-helix	72-81	10
β-strand	87-92	6	20
β-strand	98-104	7	20
β-strand	111-117	7	20
α-helix	122-125	4
β-strand	135-140	6	22
α-helix	141-154	14
β-strand	157-163	7	14
β-strand	166-172	7	14
β-strand	176-182	7	14
β-strand	196-199	4	22
β-strand	203-208	6	14
α-helix	209-214	6
α-helix	215-220	6
β-strand	224-229	6	22
α-helix	234	1
β-strand	235-240	6	22
β-strand	245-250	6	22

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
Proliferating cell nuclear antigen	F, G, H	protein	260	Saccharomyces cerevisiae	P15873
Template strand	I	DNA	40	synthetic construct
Primer strand	J	DNA	20	synthetic construct

Sequence of entity 1 (A), FASTA

>7TFJ_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

>7TFJ_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>7TFJ_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>7TFJ_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>7TFJ_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Sequence of entity 6 (F, G, H), FASTA

>7TFJ_6 Proliferating cell nuclear antigen (chains F, G, H)
ASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQ
EYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKL
MDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSG
SVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQ
FDLKSGFLQFFLAPKFNDEE

Sequence of entity 7 (I), FASTA

>7TFJ_7 Template strand (chains I)
TTTTTTTTTTTATGTACTCGTAGTGTCTGCTTTTTTTTTT

Sequence of entity 8 (J), FASTA

>7TFJ_8 Primer strand (chains J)
GCAGACACTACGAGTACATA

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	4
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. Zheng, F., Georgescu, R., Yao, N.Y. et al. Elife (2022) 11. DOI 10.7554/eLife.77469 · 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
9PEO 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
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…

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