8DR5: Open state of RFC:PCNA

Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD. Determined by electron microscopy at 2.76 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Saccharomyces cerevisiae
Chains: 12
Atoms: 22,780
Mol. weight: 366.48 kDa
Ligands: GDP, AGS, MG
Released: 17 Aug 2022

Explore 8DR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DR5 contains 175 α-helices and 126 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: 51 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	106-112	7
α-helix	150-152	3
β-strand	162-166	5	1
β-strand	168	1	2
α-helix	174-183	10
α-helix	186	1
β-strand	187-188	2	1
β-strand	198-201	4	1
β-strand	203	1	2
α-helix	207-216	10
β-strand	219-221	3	1
α-helix	223-231	9
α-helix	241-280	40
α-helix	293-295	3
α-helix	298-301	4
α-helix	314-325	12
α-helix	327-332	6
β-strand	348-352	5	3
α-helix	359-369	11
α-helix	372	1
β-strand	373-377	5	3
α-helix	385-388	4
α-helix	392-395	4
β-strand	398	1	4
α-helix	401-406	6
α-helix	414-417	4
β-strand	419-423	5	3
α-helix	426-428	3
α-helix	436-445	10
β-strand	451-455	5	3
α-helix	461-466	6
β-strand	471-474	4	3
α-helix	476-479	4
α-helix	484-494	11
β-strand	497-498	2	5
α-helix	500-502	3
α-helix	503-509	7
α-helix	514-524	11
β-strand	530-531	2	5
α-helix	536-542	7
α-helix	547-550	4
α-helix	551-558	8
β-strand	560	1	6
α-helix	561-564	4
α-helix	566-571	6
α-helix	574-583	10
α-helix	588-595	8
β-strand	599-601	3	6
α-helix	604-605	2
α-helix	610-631	22
α-helix	638-640	3
α-helix	641-644	4
α-helix	645-650	6
α-helix	651-656	6
β-strand	658-660	3	6
α-helix	663-667	5
α-helix	669-689	21
α-helix	691-693	3
α-helix	698-700	3
α-helix	701-705	5
α-helix	706-713	8
α-helix	715-719	5
α-helix	721-723	3
α-helix	724-734	11
α-helix	739-746	8
α-helix	751-753	3
α-helix	756-761	6
α-helix	764-775	12

Chain B: 26 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
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	7
α-helix	55-67	13
α-helix	68-70	3
α-helix	71-74	4
β-strand	75-78	4	7
α-helix	86-88	3
α-helix	89-93	5
α-helix	94-98	5
β-strand	99	1	8
β-strand	109-114	6	7
α-helix	116-118	3
α-helix	121-133	13
β-strand	138-144	7	7
α-helix	147-149	3
α-helix	152-157	6
β-strand	159-162	4	7
α-helix	163-167	5
α-helix	168-182	15
β-strand	186	1	9
α-helix	188-198	11
α-helix	202-214	13
β-strand	219	1	9
α-helix	221-227	7
α-helix	232-240	9
α-helix	245-251	7
α-helix	252-257	6
α-helix	263-275	13
α-helix	282-301	20
α-helix	306-319	14

Chain C: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	15-18	4
α-helix	24-26	3
α-helix	31-42	12
β-strand	49-52	4	10
α-helix	59-70	12
α-helix	75-77	3
β-strand	79-82	4	10
α-helix	90-92	3
α-helix	93-97	5
α-helix	98-102	5
β-strand	103	1	11
β-strand	112-116	5	10
α-helix	119-121	3
α-helix	124-136	13
β-strand	141-147	7	10
α-helix	150-152	3
α-helix	155-159	5
β-strand	162-165	4	10
α-helix	167-170	4
α-helix	171-185	15
β-strand	188-189	2	12
α-helix	191-201	11
α-helix	205-218	14
β-strand	226-227	2	12
α-helix	229-236	8
α-helix	238-240	3
α-helix	241-253	13
α-helix	256-270	15
α-helix	274-285	12
α-helix	293-311	19
α-helix	316-332	17

Chain D: 26 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
α-helix	36-38	3
α-helix	43-55	13
α-helix	58-60	3
β-strand	61-64	4	13
α-helix	72-83	12
β-strand	92-95	4	13
α-helix	103-105	3
α-helix	106-110	5
α-helix	111-115	5
β-strand	116	1	14
α-helix	117-122	6
α-helix	123-128	6
β-strand	135-140	6	13
α-helix	142-144	3
α-helix	147-151	5
α-helix	154-159	6
β-strand	164-170	7	13
α-helix	173-175	3
α-helix	178-183	6
β-strand	185-188	4	13
α-helix	189-191	3
β-strand	192	1	15
α-helix	198-208	11
β-strand	212	1	16
α-helix	216-224	9
β-strand	226	1	15
α-helix	228-245	18
β-strand	251	1	16
α-helix	253-259	7
α-helix	262-264	3
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: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	13-15	3
α-helix	20-31	12
α-helix	33-35	3
β-strand	39-42	4	17
α-helix	49-60	12
α-helix	63-66	4
β-strand	69-76	8	17
β-strand	82-89	8	17
β-strand	93-96	4	17
α-helix	98-104	7
α-helix	105-117	13
β-strand	119	1	18
β-strand	122	1	19
β-strand	131	1	19
α-helix	135	1
β-strand	136-140	5	17
α-helix	143-145	3
α-helix	148-152	5
α-helix	155-160	6
β-strand	165-171	7	17
α-helix	179-183	5
β-strand	186-189	4	17
α-helix	191-194	4
α-helix	195-209	15
β-strand	212-213	2	20
α-helix	217-225	9
α-helix	230-243	14
β-strand	247-248	2	20
α-helix	252-255	4
α-helix	258-272	15
α-helix	276-290	15
α-helix	296-308	13
α-helix	315-333	19
α-helix	338-352	15

Chain F: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	21
α-helix	9-17	9
β-strand	25-31	7	14
β-strand	34-40	7	14
β-strand	46-52	7	14
α-helix	54-56	3
β-strand	59-62	4	21
β-strand	66-71	6	14
α-helix	72-81	10
β-strand	87-92	6	21
β-strand	98-105	8	21
β-strand	110-117	8	21
β-strand	119	1	14
β-strand	135-140	6	14
α-helix	141-152	12
β-strand	157-163	7	22
β-strand	166-172	7	22
β-strand	176-182	7	22
β-strand	185	1	23
α-helix	191-193	3
β-strand	195	1	23
β-strand	196-199	4	14
β-strand	203-208	6	22
α-helix	209-215	7
α-helix	216-220	5
β-strand	224-229	6	14
β-strand	235-240	6	14
β-strand	245-250	6	14
α-helix	251-252	2
β-strand	253	1	11
α-helix	254-255	2

Chain G: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
α-helix	9-19	11
β-strand	25-31	7	24
β-strand	34-40	7	24
β-strand	46-53	8	24
α-helix	54-56	3
β-strand	57-59	3	22
β-strand	62	1	22
β-strand	66-71	6	24
α-helix	72-81	10
β-strand	87-92	6	22
β-strand	98-105	8	22
β-strand	110-117	8	22
α-helix	118	1
β-strand	119	1	8
α-helix	123-126	4
β-strand	135-140	6	24
α-helix	141-154	14
β-strand	157-163	7	25
β-strand	166-170	5	25
β-strand	180-182	3	25
β-strand	185	1	26
β-strand	195	1	26
β-strand	196	1	24
β-strand	203-208	6	25
α-helix	209-216	8
α-helix	219-221	3
β-strand	224-229	6	24
β-strand	235-241	7	24
β-strand	244-250	7	24
β-strand	253	1	4

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	27
α-helix	9-17	9
β-strand	25	1	28
β-strand	28-31	4	29
β-strand	34-40	7	29
β-strand	46-53	8	29
β-strand	57-62	6	27
β-strand	66-68	3	29
β-strand	71	1	28
α-helix	72-80	9
β-strand	89-91	3	30
β-strand	98-102	5	30
β-strand	114-117	4	30
β-strand	135-140	6	29
α-helix	141-154	14
β-strand	157-162	6	31
β-strand	163	1	32
β-strand	166	1	32
β-strand	169-170	2	31
β-strand	171-172	2	21
β-strand	176-181	6	21
β-strand	185	1	33
α-helix	191-193	3
β-strand	195	1	33
β-strand	196-199	4	29
β-strand	203-208	6	31
α-helix	209-217	9
α-helix	219-221	3
β-strand	224-229	6	29
β-strand	236-240	5	29
β-strand	245-250	6	29
α-helix	251-252	2
β-strand	253	1	18
α-helix	254	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Replication factor C subunit 1	A	protein	918	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	277	Saccharomyces cerevisiae	P15873
DNA (5'-d(ptptptpcpgpgpgpgpgpgpgpcp*c)-3')	I	DNA	13	Saccharomyces cerevisiae
DNA (5'-d(pgpgpcpcpcpcpcpcpcpgpgpc)-3')	J	DNA	12	Saccharomyces cerevisiae
DNA (5'-d(papgpgpgpgpgpgpgpgpgp*g)-3')	K	DNA	11	Saccharomyces cerevisiae
DNA (5'-d(pcpcpcpcpcpcpcpcpcpcptptp*t)-3')	L	DNA	13	Saccharomyces cerevisiae

Sequence of entity 1 (A), FASTA

>8DR5_1 Replication factor C subunit 1 (chains A)
MVNISDFFGKNKKSVRSSTSRPTRQVGSSKPEVIDLDTESDQESTNKTPKKMPVSNVIDV
SETPEGEKKLPLPAKRKASSPTVKPASSKKTKPSSKSSDSASNITAQDVLDKIPSLDLSN
VHVKENAKFDFKSANSNADPDEIVSEIGSFPEGKPNCLLGLTIVFTGVLPTLERGASEAL
AKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLIAGMPAEGGDG
EAAEKARRKLEEQHNIATKEAELLVKKEEERSKKLAATRVSGGHLERDNVVREEDKLWTV
KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKT
TAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFV
IIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDA
NSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEIS
KAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLMIQENYLSTR
PSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLHAVLSSVYPASKVAGHM
AGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIGLRLDYLPTFRKRLLDPFLKQ
GADAISSVIEVMDDYYLTKEDWDSIMEFFVGPDVTTAIIKKIPATVKSGFTRKYNSMTHP
VAIYRTGSTIGGGGVGTSTSTPDFEDVVDADDNPVPADDEETQDSSTDLKKDKLIKQKAK
PTKRKTATSKPGGSKKRKTKAGLNENLYFQGGGDYKDDDDKDYKDDDDKDYKDDDDKGGK
DHLIHNVHKEEHAHAHNK

Sequence of entity 2 (B), FASTA

>8DR5_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA

Sequence of entity 3 (C), FASTA

>8DR5_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Sequence of entity 4 (D), FASTA

>8DR5_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Sequence of entity 5 (E), FASTA

>8DR5_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

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

>8DR5_6 Proliferating cell nuclear antigen (chains F, G, H)
MGSSHHHHHHSSGLVPRASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVD
DSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIIL
LFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIM
ITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSL
SDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

Sequence of entity 7 (I), FASTA

>8DR5_7 DNA (5'-D(P*TP*TP*TP*CP*GP*GP*GP*GP*GP*GP*GP*CP*C)-3') (chains I)
TTTCGGGGGGGCC

Sequence of entity 8 (J), FASTA

>8DR5_8 DNA (5'-D(P*GP*GP*CP*CP*CP*CP*CP*CP*CP*GP*GP*C)-3') (chains J)
GGCCCCCCCGGC

Sequence of entity 9 (K), FASTA

>8DR5_9 DNA (5'-D(P*AP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') (chains K)
AGGGGGGGGGG

Sequence of entity 10 (L), FASTA

>8DR5_10 DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*TP*TP*T)-3') (chains L)
CCCCCCCCCCTTT

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	4
MG	Magnesium ion	Mg	4

Primary citation

Multistep loading of a DNA sliding clamp onto DNA by replication factor C. Schrecker, M., Castaneda, J.C., Devbhandari, S. et al. Elife (2022) 11. DOI 10.7554/eLife.78253 · 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…

Browse structure collections

About this viewer

MolViewer shows 8DR5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.