8FS3: Checkpoint protein RAD24

Structure of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 10-nt gapped DNA in step 1 (open 9-1-1 and shoulder bound DNA only). Determined by electron microscopy at 2.93 Å resolution. Released 14 Jun 2023.

Method
Electron microscopy
Resolution
2.93 Å
Organisms
Saccharomyces cerevisiae, synthetic construct
Chains
10
Atoms
21,222
Mol. weight
409.35 kDa
Ligands
ADP, AGS, MG
Released
14 Jun 2023

Explore 8FS3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FS3 contains 150 α-helices and 114 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, 9 β-strands

ElementResiduesLengthSheet
α-helix66-694
α-helix75-773
α-helix82-9615
β-strand104-10961
α-helix115-12511
α-helix127-1304
β-strand148-15031
α-helix162-1643
α-helix165-1739
β-strand183-18641
α-helix195-20915
β-strand219-22461
β-strand22612
α-helix227-2304
β-strand24412
α-helix246-2494
α-helix252-2554
β-strand260-26451
α-helix267-2693
α-helix270-28213
α-helix285-2906
α-helix293-2953
α-helix297-30711
α-helix311-32313
α-helix333-3375
α-helix339-34810
β-strand35013
β-strand35313
α-helix356-36611
α-helix368-3714
α-helix374-38310
α-helix384-3863
α-helix394-40714
α-helix414-43118
α-helix446-46924
α-helix477-4793
α-helix480-4845
α-helix487-49812
α-helix5381
Chain B: 24 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix11-144
α-helix20-223
α-helix27-3913
α-helix42-443
β-strand45-4954
α-helix55-6713
α-helix68-714
β-strand7514
β-strand7814
α-helix86-883
α-helix89-935
α-helix94-985
β-strand109-11464
α-helix116-1183
α-helix121-13313
β-strand138-14474
α-helix147-1493
α-helix152-1554
β-strand159-16354
α-helix164-1674
α-helix168-18215
β-strand18615
α-helix188-19811
α-helix202-21615
β-strand21915
α-helix221-2277
α-helix232-2409
α-helix245-2528
α-helix253-2575
α-helix263-27513
α-helix282-30019
α-helix306-32015
Chain C: 24 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix10-123
α-helix24-263
α-helix31-4313
β-strand49-5246
α-helix59-7012
α-helix75-784
β-strand79-8246
α-helix90-923
α-helix93-975
α-helix98-1003
β-strand10317
α-helix104-1052
β-strand112-11656
α-helix119-1213
α-helix124-13613
β-strand141-14776
α-helix150-1523
α-helix155-1595
β-strand162-16546
α-helix167-1693
α-helix171-18515
α-helix191-20111
α-helix205-21814
α-helix229-2368
α-helix241-25212
α-helix256-27015
α-helix274-28613
α-helix294-31219
α-helix316-33015
α-helix332-3354
Chain D: 25 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix27-304
α-helix43-5412
β-strand61-6448
α-helix71-9121
β-strand92-9548
α-helix103-1053
α-helix106-1105
α-helix111-1155
β-strand11619
α-helix117-1215
α-helix123-1286
β-strand135-14068
α-helix142-1443
α-helix147-15913
β-strand164-17078
α-helix173-1753
α-helix178-1836
β-strand185-18848
α-helix189-1913
α-helix194-20714
β-strand212110
β-strand214-217411
α-helix219-2235
α-helix228-24518
α-helix2501
β-strand251110
α-helix2521
α-helix253-2597
α-helix262-2643
α-helix265-27612
α-helix280-29213
α-helix297-31014
α-helix316-33318
α-helix339-35113
Chain E: 20 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix4-74
α-helix21-3111
α-helix33-353
β-strand39-42412
α-helix49-6113
β-strand69-76812
β-strand82-90912
β-strand93-96412
α-helix98-1003
α-helix105-11814
β-strand122113
β-strand133113
α-helix1351
β-strand136-140512
α-helix143-1453
α-helix150-16011
β-strand165-171712
α-helix179-1835
β-strand186-189412
α-helix191-1944
α-helix195-20915
β-strand212-213214
α-helix217-22610
α-helix230-24213
β-strand247-248214
α-helix253-2553
α-helix258-27215
α-helix276-29116
α-helix296-30712
α-helix315-33420
α-helix338-35316
Chain F: 10 helices, 25 β-strands
ElementResiduesLengthSheet
β-strand2-3215
β-strand4-7416
α-helix13-2917
β-strand33-38617
β-strand41-46617
β-strand67-73717
α-helix74-763
β-strand79116
β-strand82-83215
α-helix87-893
β-strand91117
β-strand93-95317
α-helix97-11115
β-strand119-122416
β-strand155-162816
β-strand201-208816
β-strand209-211317
α-helix214-2185
α-helix222-2243
β-strand231-235517
α-helix236-2372
α-helix241-25111
α-helix252-2554
β-strand261-267718
β-strand280-285618
β-strand290-294518
β-strand296119
β-strand301117
β-strand405118
β-strand408-411418
α-helix412-42312
β-strand427-433717
β-strand437-444817
β-strand462-469817
β-strand472118
Chain G: 11 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand11-15518
α-helix18-2710
β-strand36-4279
β-strand45-5289
β-strand56-6389
α-helix64-663
β-strand69-70218
β-strand80-8569
α-helix86-927
β-strand105-110618
α-helix1161
β-strand117-122618
β-strand126119
β-strand127-132618
β-strand13519
β-strand154-15969
α-helix160-17314
β-strand177-183720
β-strand191-197720
β-strand202-207620
α-helix2081
β-strand216-21949
β-strand220121
β-strand227121
β-strand233-238620
α-helix239-2424
α-helix243-2453
α-helix246-2516
β-strand254-25969
β-strand264-27189
β-strand304-31189
α-helix3121
β-strand31317
α-helix319-32911
Chain H: 6 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand3-7520
α-helix10-2617
β-strand29-34622
β-strand38-44722
β-strand50-57822
β-strand66120
β-strand93-97522
α-helix98-1025
β-strand113-120820
β-strand133123
β-strand135-140620
β-strand145-148420
β-strand151123
β-strand152-153222
β-strand228-233622
α-helix234-24310
β-strand251-256624
β-strand260-266724
β-strand270-271225
β-strand277-279325
β-strand284-289624
β-strand295-297322
β-strand321-324424
α-helix327-3359
α-helix336-3383
β-strand348-353622
β-strand359-365722
β-strand369-376822
α-helix377-3782

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Checkpoint protein RAD24Aprotein545Saccharomyces cerevisiaeP32641 (AlphaFold model)
Replication factor C subunit 4Bprotein323Saccharomyces cerevisiaeP40339 (AlphaFold model)
Replication factor C subunit 3Cprotein336Saccharomyces cerevisiaeP38629 (AlphaFold model)
Replication factor C subunit 2Dprotein353Saccharomyces cerevisiaeP40348 (AlphaFold model)
Replication factor C subunit 5Eprotein354Saccharomyces cerevisiaeP38251
DNA damage checkpoint control protein MEC3Fprotein474Saccharomyces cerevisiaeQ02574
DNA damage checkpoint control protein RAD17Gprotein401Saccharomyces cerevisiaeP48581
DDC1 isoform 1Hprotein612Saccharomyces cerevisiaeQ08949
Template strandIDNA50synthetic construct
Primer strand 2KDNA20synthetic construct
Sequence of entity 1 (A), FASTA
>8FS3_1 Checkpoint protein RAD24 (chains A)
MDSTNLNKRPLLQYSLSSLGSQITKWSSSRPTSPVRKARSTENDFLSKQDTSSILPSIND
DGGEQWYEKFKPNCLEQVAIHKRKLKDVQEALDAMFLPNAKHRILLLSGPSGCSKSTVIK
ELSKILVPKYRQNSNGTSFRSTPNEHKVTEFRGDCIVNDLPQMESFSEFLKGARYLVMSN
LSLILIEDLPNVFHIDTRRRFQQLILQWLYSSEPLLPPLVICITECEIPENDNNYRKFGI
DYTFSAETIMNKEILMHPRLKRIKFNPINSTLLKKHLKFICVQNMKMLKEKNKWNKRQEV
IDYIAQETGDIRSAITTLQFWATSSGSLPISTRESTISYFHAIGKVIHGSHSTNNDNEMI
NNLFENSNNLLSKEDFKLGILENYNTFNKGEFSISDASSIVDCLSECDNMNGLPESNEYG
LREVRKTFRNISKQGHNHGTVYFPREWKVRKLQNSFKVQAEDWLNVSLYKYNAVHSFRNI
TLEFGYYAPLIRKCQSYKKKYILYYLKNLPSGSSGPKQTMDKFSDIMKVENGIDVVDRIG
GPIEA
Sequence of entity 2 (B), FASTA
>8FS3_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA
Sequence of entity 3 (C), FASTA
>8FS3_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETV
Sequence of entity 4 (D), FASTA
>8FS3_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
Sequence of entity 5 (E), FASTA
>8FS3_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD
Sequence of entity 6 (F), FASTA
>8FS3_6 DNA damage checkpoint control protein MEC3 (chains F)
MKLKLIVNGCEAPDDYKLLRTTINTVASLRKTAILRFNSERLTIISTPKSSLNSSNNGTI
LRGDTGQLWCTIPHDVFRLYTVISARELNTITMECNCDSLLSVFKRYDRVMNQGSSSNMT
IKLQSMPEWNTNNGTLSGGTAGGVDTTSKPNPICALGITFEEIVHTSGPNDAIVMNGGVD
EHNGLPTTVGTGNLLASNKVIMHSFKVPVKLLFRAQDTRIQEPMINYIQLMMYKLPPISG
EFGSAFHGFIRRVERYSNVNHIHLMGVKKKEHGNEGDDVELKIIVNELDWHLEICWNGPL
DSVIQRQEGLTDNPSQNQHIDTDGRQEEGSLPIIEADKPMSSLYTNTRDREMEENIRYDE
DLLRIEDSSIADTRGNIYTADTSGDTEFNDISVMVEKAEQESSSTHEVIIRCKDWKVCSK
LYAAFEEVVLAISHDESCVFHCSLDRGSLEDSEDVEKPRERGQIIYYIARSKGL
Sequence of entity 7 (G), FASTA
>8FS3_7 DNA damage checkpoint control protein RAD17 (chains G)
MRINSELANKFSASTVHLEHITTALSCLTPFGSKDDVLIFIDADGLSFVRENNHVIKIQL
LLSRELFMSYSYRNETEDHMKLCVKINHILDSVSVMNRNSDDIVECTLSYDGHGSPFVLI
FEDSFISERVEYSTYLIKDFDTNGLELDRERISFEAIIKGEALHSALKDLKEIGCKECYV
YAKTEANDENVFALISKSQLGFSKIKLPSNRSILEKLQVFDGDSTTVIDGFAVIGFFDFT
SFDKIRKSTKIASKVLFRMDVHGVLSVNILSQTDDVIITDTTRPSNNRPGSIRQLQLPKD
YPGIVIEVCMLEKESIDEAAQTEIELLMETNELGNRNSFKKSTIRKRYGTDKGNETSNDN
LLQLNGKKIKLPSEEENNKNRESEDEENHCKYPTKDIPIFF
Sequence of entity 8 (H), FASTA
>8FS3_8 DDC1 isoform 1 (chains H)
MSFKATITESGKQNIWFRAIYVLSTIQDDIKITVTTNELIAWSMNETDTTLCQVRFQKSF
FEEYEFKPHEIVFGENGVQVIEDTYGNSHKLYSFRVNGRHLTTISRKPDGDGIKSFTIAV
NNTSTCPESLANRLIVVIEMDSLIVKEYCPQFQPIKYDPIIINLKYKRRFLDVFGTAASD
RNPQEPLDPKLLDVFTNTERELTSALFNEEVESDIRKRNQLTAADEINYICCNSTLLKNF
LDNCNVNVTDEVKLEINVHRLSITAFTKAVYGKNNDLLRNALSMSNTISTLDLEHYCLFT
TIEDEKQDKRSHSKRREHMKSIIFKLKDFKNFITIGPSWKTTQDGNDNISLWFCHPGDPI
LMQMQKPGVKLELVEVTDSNINDDILEGKFIKTAISGSKEEAGLKDNKESCESPLKSKTA
LKRENLPHSVAGTRNSPLKVSYLTPDNGSTVAKTYRNNTARKLFVEEQSQSTNYEQDKRF
RQASSVHMNMNREQSFDIGTTHEVACPRNESNSLKRSIADICNETEDPTQQSTFAKRADT
TVTWGKALPAADDEVSCSNIDRKGMLKKEKLKHMQGLLNSQNDTSNHKKQDNKEMEDGLG
LTQVEKPRGIFD
Sequence of entity 9 (I), FASTA
>8FS3_9 Template strand (chains I)
CGGTATAGGCGATACGAATCTTTTTTTTTTCCGTATAGCCGTAGCGAGCC
Sequence of entity 10 (K), FASTA
>8FS3_10 Primer strand 2 (chains K)
GATTCGTATCGCCTATACCG

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S4
MGMagnesium ionMg4

Primary citation

Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology. Zheng, F., Georgescu, R.E., Yao, N.Y. et al. Cell Rep (2023) 42:112694-112694. DOI 10.1016/j.celrep.2023.112694 · PubMed

Other PDB entries of the same protein (UniProt P32641 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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