8DQX: Open state of RFC:PCNA

Open state of RFC:PCNA bound to a 3' ss/dsDNA junction. Determined by electron microscopy at 2.1 Å resolution. Released 24 Aug 2022.

Method
Electron microscopy
Resolution
2.1 Å
Organism
Saccharomyces cerevisiae
Chains
11
Atoms
22,030
Mol. weight
346.89 kDa
Ligands
MG, GDP, AGS
Released
24 Aug 2022

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

Secondary structure: helices and β-sheets

8DQX contains 176 α-helices and 115 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: 41 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix293-2953
α-helix298-3014
α-helix307-3093
α-helix314-32512
α-helix327-3326
β-strand348-35251
α-helix359-36911
β-strand373-37751
α-helix385-3906
α-helix392-3954
β-strand39812
α-helix401-4066
β-strand419-42351
α-helix426-4283
α-helix431-4333
α-helix436-44611
β-strand451-45551
α-helix461-4666
β-strand471-47441
α-helix477-4793
α-helix480-49415
β-strand497-49823
α-helix500-50910
α-helix514-52411
β-strand530-53123
α-helix536-5427
α-helix547-5504
α-helix551-5588
β-strand56014
α-helix562-5643
α-helix566-5716
α-helix574-58310
α-helix588-5958
β-strand599-60134
α-helix604-6052
α-helix610-63122
α-helix638-6403
α-helix641-6444
α-helix645-6506
α-helix651-6566
β-strand658-66034
α-helix669-69022
α-helix698-7003
α-helix701-7055
α-helix706-7138
α-helix715-7206
α-helix721-7244
α-helix725-73410
α-helix739-7479
α-helix751-7533
α-helix756-7616
α-helix764-77512
Chain B: 30 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix8-103
α-helix11-144
α-helix20-223
α-helix27-3913
α-helix42-443
β-strand45-4845
α-helix55-6713
α-helix68-703
α-helix71-744
β-strand75-7845
α-helix86-883
α-helix89-935
α-helix94-985
β-strand9916
β-strand109-11465
α-helix116-1183
α-helix121-1255
α-helix128-1336
β-strand138-14475
α-helix147-1493
α-helix152-1565
β-strand159-16245
α-helix163-1675
α-helix168-18215
β-strand18617
α-helix188-19811
α-helix202-21615
β-strand21917
α-helix221-2277
α-helix229-2313
α-helix232-24110
α-helix245-2517
α-helix252-2565
α-helix257-2593
α-helix263-27513
α-helix282-29817
α-helix299-3035
α-helix306-31914
Chain C: 23 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix10-123
α-helix15-184
α-helix24-263
α-helix31-4313
β-strand49-5248
α-helix59-7113
α-helix72-776
β-strand79-8248
α-helix90-923
α-helix93-975
α-helix98-1014
β-strand10319
β-strand112-11658
α-helix119-1213
α-helix124-13613
β-strand141-14778
α-helix150-1523
α-helix155-1606
β-strand162-16548
α-helix166-1705
α-helix171-18515
β-strand189110
α-helix191-20111
α-helix205-21814
β-strand227110
α-helix229-2368
α-helix241-25313
α-helix256-27015
α-helix274-28613
α-helix293-31119
α-helix316-33217
Chain D: 27 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix27-304
α-helix36-383
α-helix43-5513
α-helix58-603
β-strand61-64411
α-helix71-9121
β-strand92-95411
α-helix103-1053
α-helix106-1105
α-helix111-1155
β-strand116112
α-helix117-1226
α-helix123-1286
β-strand135-139511
α-helix142-1443
α-helix147-15913
β-strand164-170711
α-helix173-1753
α-helix178-1836
β-strand185-188411
α-helix189-1913
β-strand192113
α-helix194-20714
β-strand212114
α-helix216-2249
β-strand226113
α-helix228-24518
α-helix249-2502
β-strand251114
α-helix2521
α-helix253-2597
α-helix262-2643
α-helix265-27713
α-helix280-29112
α-helix297-30913
α-helix316-33419
α-helix339-35113
Chain E: 24 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix4-74
α-helix13-153
α-helix20-3112
α-helix33-353
α-helix36-383
β-strand39-42415
α-helix49-6113
α-helix63-664
β-strand69-76815
β-strand82-89815
β-strand93-96415
α-helix98-1047
α-helix105-1073
α-helix108-1136
α-helix114-1185
β-strand119116
β-strand122117
β-strand131117
β-strand136-140515
α-helix143-1453
α-helix148-16013
β-strand165-171715
α-helix179-1835
β-strand186-189415
α-helix191-1944
α-helix195-20814
β-strand212-213218
α-helix217-2259
α-helix230-24314
β-strand247-248218
α-helix252-2576
α-helix258-27215
α-helix276-29116
α-helix296-30712
α-helix315-33420
α-helix338-35215
Chain F: 11 helices, 22 β-strands
ElementResiduesLengthSheet
β-strand2-6519
α-helix9-179
α-helix20-223
β-strand25-31712
β-strand34-40712
β-strand46-53812
α-helix54-563
β-strand59-62419
β-strand66-71612
α-helix72-8110
β-strand87-92619
β-strand98-104719
β-strand111-117719
α-helix1181
β-strand119112
β-strand135-140612
α-helix141-15212
β-strand157-163720
β-strand166-172720
β-strand176-182720
β-strand185121
α-helix191-1933
β-strand195121
β-strand196-199412
β-strand203-208620
α-helix209-2157
α-helix216-2216
β-strand224-229612
β-strand235-240612
β-strand245-250612
α-helix251-2522
β-strand25319
α-helix2541
Chain G: 11 helices, 20 β-strands
ElementResiduesLengthSheet
β-strand2-6520
α-helix10-1910
α-helix20-223
β-strand25-31722
β-strand34-40722
β-strand46-53822
α-helix54-563
β-strand59-62420
β-strand66-71622
α-helix72-809
β-strand87-92620
β-strand98-105820
β-strand110-117820
β-strand11916
α-helix124-1274
α-helix129-1313
β-strand135-140622
α-helix141-15414
β-strand157-163723
β-strand166-173823
β-strand176-182723
α-helix191-1933
β-strand196-199422
β-strand203-208623
α-helix209-2157
α-helix216-2216
β-strand224-229622
α-helix2341
β-strand235-240622
β-strand244-250722
β-strand25312
Chain H: 9 helices, 24 β-strands
ElementResiduesLengthSheet
β-strand2-6524
α-helix9-1911
β-strand25-30625
β-strand34126
β-strand35-40625
β-strand46-50525
β-strand53126
β-strand57-62624
β-strand66-71625
α-helix72-8110
β-strand87-92624
β-strand98-104724
β-strand111-117724
β-strand119125
β-strand135-140625
α-helix141-15212
β-strand157-163719
β-strand166-172719
β-strand176-182719
β-strand185127
α-helix191-1933
β-strand195127
β-strand196-199425
β-strand203-208619
α-helix209-2157
α-helix216-2205
β-strand224-229625
α-helix2341
β-strand235-240625
β-strand245-250625
α-helix251-2522
β-strand253116
α-helix2541

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Replication factor C subunit 1Aprotein861Saccharomyces cerevisiaeP38630 (AlphaFold model)
Replication factor C subunit 4Bprotein323Saccharomyces cerevisiaeP40339 (AlphaFold model)
Replication factor C subunit 3Cprotein340Saccharomyces cerevisiaeP38629 (AlphaFold model)
Replication factor C subunit 2Dprotein353Saccharomyces cerevisiaeP40348 (AlphaFold model)
Replication factor C subunit 5Eprotein354Saccharomyces cerevisiaeP38251
Proliferating cell nuclear antigenF, G, Hprotein259Saccharomyces cerevisiaeP15873
DNA (5'-d(*tp*tp*tp*tp*tp*t)-3')IDNA6Saccharomyces cerevisiae
DNA (5'-d(p*tp*cp*cp*gp*ap*gp*cp*gp*ap*a)-3')JDNA10Saccharomyces cerevisiae
DNA (5'-d(p*tp*tp*tp*gp*cp*cp*cp*gp*gp*a)-3')KDNA10Saccharomyces cerevisiae
Sequence of entity 1 (A), FASTA
>8DQX_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
>8DQX_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA
Sequence of entity 3 (C), FASTA
>8DQX_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV
Sequence of entity 4 (D), FASTA
>8DQX_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
Sequence of entity 5 (E), FASTA
>8DQX_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD
Sequence of entity 6 (F, G, H), FASTA
>8DQX_6 Proliferating cell nuclear antigen (chains F, G, H)
SMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQE
YRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLM
DIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGS
VIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQF
DLKSGFLQFFLAPKFNDEE
Sequence of entity 7 (I), FASTA
>8DQX_7 DNA (5'-D(*TP*TP*TP*TP*TP*T)-3') (chains I)
TTTTTT
Sequence of entity 8 (J), FASTA
>8DQX_8 DNA (5'-D(P*TP*CP*CP*GP*AP*GP*CP*GP*AP*A)-3') (chains J)
TCCGAGCGAA
Sequence of entity 9 (K), FASTA
>8DQX_9 DNA (5'-D(P*TP*TP*TP*GP*CP*CP*CP*GP*GP*A)-3') (chains K)
TTTGCCCGGA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg4
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P21
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S4

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:

Browse structure collections

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