7U1P: RFC:PCNA

RFC:PCNA bound to DNA with a ssDNA gap of five nucleotides. Determined by electron microscopy at 3.0 Å resolution. Released 6 Jul 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Saccharomyces cerevisiae, synthetic construct
Chains: 11
Atoms: 22,727
Mol. weight: 369.57 kDa
Ligands: ADP, MG, AGS
Released: 6 Jul 2022

Explore 7U1P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U1P contains 161 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: 48 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	150-152	3
β-strand	162-164	3	1
α-helix	174-182	9
β-strand	187-188	2	1
β-strand	198-200	3	1
α-helix	207-216	10
β-strand	219-221	3	1
α-helix	223-232	10
α-helix	234	1
α-helix	241-276	36
α-helix	293-295	3
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	2
α-helix	359-370	12
α-helix	372	1
β-strand	373-378	6	2
α-helix	385-396	12
β-strand	398	1	3
α-helix	401-405	5
α-helix	414-416	3
β-strand	419-424	6	2
α-helix	426-428	3
α-helix	430-431	2
α-helix	436-445	10
β-strand	451-455	5	2
α-helix	461-466	6
β-strand	470-474	5	2
α-helix	475-479	5
α-helix	480-493	14
β-strand	497-498	2	4
α-helix	500-502	3
α-helix	503-510	8
α-helix	514-524	11
β-strand	530-531	2	4
α-helix	536-543	8
α-helix	547-550	4
α-helix	551-558	8
α-helix	566-571	6
α-helix	574-583	10
α-helix	588-595	8
β-strand	599-601	3	5
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	651-655	5
β-strand	658-660	3	5
α-helix	665-667	3
α-helix	669-689	21
α-helix	698-700	3
α-helix	701-705	5
α-helix	706-719	14
α-helix	722-724	3
α-helix	725-734	10
α-helix	739-746	8
α-helix	751-753	3
α-helix	756-761	6
α-helix	764-777	14

Chain B: 27 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-14	4
α-helix	20-22	3
α-helix	27-39	13
α-helix	42-44	3
β-strand	45-48	4	6
α-helix	56-67	12
α-helix	68-70	3
α-helix	71-74	4
β-strand	75-77	3	6
α-helix	86-87	2
α-helix	88-93	6
α-helix	94-98	5
β-strand	99	1	7
β-strand	109-113	5	6
α-helix	116-118	3
α-helix	121-133	13
β-strand	138-144	7	6
α-helix	147-149	3
α-helix	152-156	5
β-strand	159-162	4	6
α-helix	165-167	3
α-helix	168-182	15
β-strand	186	1	8
α-helix	188-198	11
α-helix	202-215	14
β-strand	219	1	8
α-helix	221-227	7
α-helix	229-231	3
α-helix	232-240	9
α-helix	245-251	7
α-helix	252-257	6
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	24-26	3
α-helix	31-43	13
β-strand	49-52	4	9
α-helix	59-71	13
β-strand	79-83	5	9
α-helix	90-92	3
α-helix	93-97	5
α-helix	98-102	5
β-strand	103	1	10
β-strand	112-117	6	9
α-helix	119-121	3
α-helix	124-136	13
β-strand	141-146	6	9
β-strand	162-165	4	9
α-helix	167-169	3
α-helix	171-184	14
β-strand	189	1	11
α-helix	191-201	11
α-helix	205-218	14
β-strand	227	1	11
α-helix	229-236	8
α-helix	238-240	3
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: 24 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	15-23	9
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	12
α-helix	71-83	13
α-helix	85-91	7
β-strand	92-95	4	12
α-helix	103-104	2
α-helix	105-110	6
α-helix	111-115	5
β-strand	116	1	13
α-helix	117-122	6
α-helix	123-128	6
β-strand	135-140	6	12
α-helix	142-144	3
α-helix	147-159	13
β-strand	164-170	7	12
α-helix	178-183	6
β-strand	185-188	4	12
β-strand	192	1	14
α-helix	194-207	14
β-strand	212	1	15
α-helix	216-224	9
β-strand	226	1	14
α-helix	228-245	18
β-strand	251	1	15
α-helix	253-259	7
α-helix	265-276	12
α-helix	280-290	11
α-helix	297-310	14
α-helix	316-333	18
α-helix	339-352	14

Chain E: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	20-31	12
β-strand	39-42	4	16
α-helix	49-60	12
α-helix	63-66	4
β-strand	69-76	8	16
β-strand	82-89	8	16
β-strand	93-96	4	16
α-helix	105-108	4
α-helix	109-113	5
α-helix	114-119	6
β-strand	136-140	5	16
α-helix	148-160	13
β-strand	165-170	6	16
α-helix	179-184	6
β-strand	186-189	4	16
α-helix	191-194	4
α-helix	195-209	15
β-strand	212-213	2	17
α-helix	217-224	8
α-helix	230-243	14
β-strand	247-248	2	17
α-helix	252-254	3
α-helix	258-272	15
α-helix	276-290	15
α-helix	296-308	13
α-helix	315-333	19
α-helix	339-352	14

Chain F: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	18
α-helix	9-19	11
β-strand	25-30	6	19
β-strand	35-40	6	19
β-strand	46-51	6	19
β-strand	57-59	3	18
β-strand	62	1	18
β-strand	66-71	6	19
α-helix	72-79	8
β-strand	87-92	6	18
β-strand	99-105	7	18
β-strand	110-116	7	18
β-strand	119	1	13
β-strand	135-140	6	19
α-helix	141-151	11
β-strand	157-163	7	20
β-strand	166-172	7	20
β-strand	176-182	7	20
α-helix	191-193	3
β-strand	196-199	4	19
β-strand	203-208	6	20
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	19
β-strand	235-240	6	19
β-strand	245-250	6	19
α-helix	252	1
β-strand	253	1	10
α-helix	254	1

Chain G: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	20
α-helix	9-18	10
β-strand	25-31	7	21
β-strand	34-40	7	21
β-strand	46-53	8	21
α-helix	54-56	3
β-strand	57-59	3	20
β-strand	62	1	20
β-strand	66-71	6	21
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	118	1
β-strand	119	1	7
β-strand	135-140	6	21
α-helix	141-154	14
β-strand	157-162	6	22
β-strand	167-172	6	22
β-strand	177-182	6	22
β-strand	196-199	4	21
β-strand	203-208	6	22
α-helix	209-216	8
β-strand	224-229	6	21
α-helix	234	1
β-strand	235-240	6	21
β-strand	244-250	7	21
α-helix	251	1
β-strand	252	1	22
β-strand	253	1	3
α-helix	254	1

Chain H: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	22
α-helix	9-17	9
β-strand	25-30	6	23
β-strand	35-40	6	23
β-strand	46-52	7	23
α-helix	54-56	3
β-strand	59-62	4	22
β-strand	66-71	6	23
α-helix	72-79	8
β-strand	87-92	6	22
β-strand	98-104	7	22
β-strand	110-117	8	22
β-strand	135-140	6	23
α-helix	141-151	11
β-strand	157-162	6	18
β-strand	167-170	4	18
β-strand	176-182	7	18
β-strand	196-199	4	23
β-strand	203-208	6	18
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	23
β-strand	235-240	6	23
β-strand	244-250	7	23

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	264	Saccharomyces cerevisiae	P15873
DNA - Primer	I	DNA	25	synthetic construct
DNA - Template	J	DNA	50	synthetic construct
DNA - non primer	K	DNA	20	synthetic construct

Sequence of entity 1 (A), FASTA

>7U1P_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

>7U1P_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>7U1P_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>7U1P_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>7U1P_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

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

>7U1P_6 Proliferating cell nuclear antigen (chains F, G, H)
GPHMASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGV
EAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEY
SLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGD
IGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAP
ALFQFDLKSGFLQFFLAPKFNDEE

Sequence of entity 7 (I), FASTA

>7U1P_7 DNA - Primer (chains I)
GGGACGCACGCGGCATTCAAGGACT

Sequence of entity 8 (J), FASTA

>7U1P_8 DNA - Template (chains J)
TTGTGGGTAGATAAATACAGACCTAAGTCCTTGAATGCCGCGTGCGTCCC

Sequence of entity 9 (K), FASTA

>7U1P_9 DNA - non primer (chains K)
CTGTATTTATCTACCCACAA

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	4
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	3

Primary citation

A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA. Liu, X., Gaubitz, C., Pajak, J. et al. Elife (2022) 11. DOI 10.7554/eLife.77483 · 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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