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- EMDB-27662: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-27662
TitleOpen state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Map dataOpen state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Sample
  • Complex: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
    • Protein or peptide: x 7 types
    • DNA: x 2 types
  • Protein or peptide: x 1 types
  • Ligand: x 4 types
KeywordsDNA damage checkpoint / REPLICATION-DNA complex
Function / homology
Function and homology information


meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / DNA clamp loader activity / Polymerase switching / telomere maintenance via recombination ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / DNA clamp unloading / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / DNA clamp loader activity / Polymerase switching / telomere maintenance via recombination / nuclease activity / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / reciprocal meiotic recombination / recombinational repair / mitotic intra-S DNA damage checkpoint signaling / sister chromatid cohesion / mitotic sister chromatid cohesion / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / subtelomeric heterochromatin formation / mismatch repair / telomere maintenance / meiotic cell cycle / DNA damage checkpoint signaling / nucleotide-excision repair / double-strand break repair via homologous recombination / DNA-templated DNA replication / double-strand break repair / site of double-strand break / double-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / cell cycle / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
Ddc1 / DNA damage checkpoint control protein Rad17 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Rad9/Ddc1 / Repair protein Rad1/Rec1/Rad17 / Replication factor C, C-terminal ...Ddc1 / DNA damage checkpoint control protein Rad17 / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Rad9/Ddc1 / Repair protein Rad1/Rec1/Rad17 / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DDC1 isoform 1 / DNA damage checkpoint control protein RAD17 / RAD24 isoform 1 / Replication factor C subunit 5 / Replication factor C subunit 3 / Replication factor C subunit 4 / Replication factor C subunit 2 / DNA damage checkpoint control protein MEC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSchrecker M / Hite RK
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA008748 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107239 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127428 United States
CitationJournal: Elife / Year: 2022
Title: Multistep loading of a DNA sliding clamp onto DNA by replication factor C.
Authors: Marina Schrecker / Juan C Castaneda / Sujan Devbhandari / Charanya Kumar / Dirk Remus / Richard K Hite /
Abstract: The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader ...The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3' end (3' ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3' ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA.
History
DepositionJul 20, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27662.png

Downloads & links

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Map

FileDownload / File: emd_27662.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOpen state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Voxel sizeX=Y=Z: 0.826 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.757545 - 3.1117527
Average (Standard dev.)-0.0013081067 (±0.049964584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Density-modified and 1.5x resampled map for model building

Fileemd_27662_additional_1.map
AnnotationDensity-modified and 1.5x resampled map for model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_27662_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_27662_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

EntireName: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
Components
  • Complex: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: DNA damage checkpoint control protein RAD17
    • Protein or peptide: DDC1 isoform 1
    • Protein or peptide: DNA damage checkpoint control protein MEC3
    • Protein or peptide: RAD24 isoform 1
    • DNA: DNA (50-MER)
    • DNA: DNA (5'-D(P*CP*GP*TP*CP*CP*CP*TP*TP*CP*C)-3')
  • Protein or peptide: Replication factor C subunit 3
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

SupramoleculeName: Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.201039 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSKTLSLQLP WVEKYRPQVL SDIVGNKETI DRLQQIAKDG NMPHMIISGM PGIGKTTSVH CLAHELLGRS YADGVLELNA SDDRGIDVV RNQIKHFAQK KLHLPPGKHK IVILDEADSM TAGAQQALRR TMELYSNSTR FAFACNQSNK IIEPLQSRCA I LRYSKLSD ...String:
MSKTLSLQLP WVEKYRPQVL SDIVGNKETI DRLQQIAKDG NMPHMIISGM PGIGKTTSVH CLAHELLGRS YADGVLELNA SDDRGIDVV RNQIKHFAQK KLHLPPGKHK IVILDEADSM TAGAQQALRR TMELYSNSTR FAFACNQSNK IIEPLQSRCA I LRYSKLSD EDVLKRLLQI IKLEDVKYTN DGLEAIIFTA EGDMRQAINN LQSTVAGHGL VNADNVFKIV DSPHPLIVKK ML LASNLED SIQILRTDLW KKGYSSIDIV TTSFRVTKNL AQVKESVRLE MIKEIGLTHM RILEGVGTYL QLASMLAKIH KLN NKA

UniProtKB: Replication factor C subunit 4

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Macromolecule #2: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 38.254543 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSTSTEKRSK ENLPWVEKYR PETLDEVYGQ NEVITTVRKF VDEGKLPHLL FYGPPGTGKT STIVALAREI YGKNYSNMVL ELNASDDRG IDVVRNQIKD FASTRQIFSK GFKLIILDEA DAMTNAAQNA LRRVIERYTK NTRFCVLANY AHKLTPALLS R CTRFRFQP ...String:
MSTSTEKRSK ENLPWVEKYR PETLDEVYGQ NEVITTVRKF VDEGKLPHLL FYGPPGTGKT STIVALAREI YGKNYSNMVL ELNASDDRG IDVVRNQIKD FASTRQIFSK GFKLIILDEA DAMTNAAQNA LRRVIERYTK NTRFCVLANY AHKLTPALLS R CTRFRFQP LPQEAIERRI ANVLVHEKLK LSPNAEKALI ELSNGDMRRV LNVLQSCKAT LDNPDEDEIS DDVIYECCGA PR PSDLKAV LKSILEDDWG TAHYTLNKVR SAKGLALIDL IEGIVKILED YELQNEETRV HLLTKLADIE YSISKGGNDQ IQG SAVIGA IKASFENETV KANV

UniProtKB: Replication factor C subunit 3

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Macromolecule #3: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.794473 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFEGFGPNKK RKISKLAAEQ SLAQQPWVEK YRPKNLDEVT AQDHAVTVLK KTLKSANLPH MLFYGPPGTG KTSTILALTK ELYGPDLMK SRILELNASD ERGISIVREK VKNFARLTVS KPSKHDLENY PCPPYKIIIL DEADSMTADA QSALRRTMET Y SGVTRFCL ...String:
MFEGFGPNKK RKISKLAAEQ SLAQQPWVEK YRPKNLDEVT AQDHAVTVLK KTLKSANLPH MLFYGPPGTG KTSTILALTK ELYGPDLMK SRILELNASD ERGISIVREK VKNFARLTVS KPSKHDLENY PCPPYKIIIL DEADSMTADA QSALRRTMET Y SGVTRFCL ICNYVTRIID PLASRCSKFR FKALDASNAI DRLRFISEQE NVKCDDGVLE RILDISAGDL RRGITLLQSA SK GAQYLGD GKNITSTQVE ELAGVVPHDI LIEIVEKVKS GDFDEIKKYV NTFMKSGWSA ASVVNQLHEY YITNDNFDTN FKN QISWLL FTTDSRLNNG TNEHIQLLNL LVKISQL

UniProtKB: Replication factor C subunit 2

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Macromolecule #4: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.993582 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSLWVDKYRP KSLNALSHNE ELTNFLKSLS DQPRDLPHLL LYGPNGTGKK TRCMALLESI FGPGVYRLKI DVRQFVTASN RKLELNVVS SPYHLEITPS DMGNNDRIVI QELLKEVAQM EQVDFQDSKD GLAHRYKCVI INEANSLTKD AQAALRRTME K YSKNIRLI ...String:
MSLWVDKYRP KSLNALSHNE ELTNFLKSLS DQPRDLPHLL LYGPNGTGKK TRCMALLESI FGPGVYRLKI DVRQFVTASN RKLELNVVS SPYHLEITPS DMGNNDRIVI QELLKEVAQM EQVDFQDSKD GLAHRYKCVI INEANSLTKD AQAALRRTME K YSKNIRLI MVCDSMSPII APIKSRCLLI RCPAPSDSEI STILSDVVTN ERIQLETKDI LKRIAQASNG NLRVSLLMLE SM ALNNELA LKSSSPIIKP DWIIVIHKLT RKIVKERSVN SLIECRAVLY DLLAHCIPAN IILKELTFSL LDVETLNTTN KSS IIEYSS VFDERLSLGN KAIFHLEGFI AKVMCCLD

UniProtKB: Replication factor C subunit 5

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Macromolecule #5: DNA damage checkpoint control protein RAD17

MacromoleculeName: DNA damage checkpoint control protein RAD17 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.637527 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MRINSELANK FSASTVHLEH ITTALSCLTP FGSKDDVLIF IDADGLSFVR ENNHVIKIQL LLSRELFMSY SYRNETEDHM KLCVKINHI LDSVSVMNRN SDDIVECTLS YDGHGSPFVL IFEDSFISER VEYSTYLIKD FDTNGLELDR ERISFEAIIK G EALHSALK ...String:
MRINSELANK FSASTVHLEH ITTALSCLTP FGSKDDVLIF IDADGLSFVR ENNHVIKIQL LLSRELFMSY SYRNETEDHM KLCVKINHI LDSVSVMNRN SDDIVECTLS YDGHGSPFVL IFEDSFISER VEYSTYLIKD FDTNGLELDR ERISFEAIIK G EALHSALK DLKEIGCKEC YVYAKTEAND ENVFALISKS QLGFSKIKLP SNRSILEKLQ VFDGDSTTVI DGFAVIGFFD FT SFDKIRK STKIASKVLF RMDVHGVLSV NILSQTDDVI ITDTTRPSNN RPGSIRQLQL PKDYPGIVIE VCMLEKESID EAA QTEIEL LMETNELGNR NSFKKSTIRK RYGTDKGNET SNDNLLQLNG KKIKLPSEEE NNKNRESEDE ENHCKYPTKD IPIF F

UniProtKB: DNA damage checkpoint control protein RAD17

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Macromolecule #6: DDC1 isoform 1

MacromoleculeName: DDC1 isoform 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 73.850672 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDYKDDDDKD YKDDDDKDYK DDDDKLEVLF QGPGMSFKAT ITESGKQNIW FRAIYVLSTI QDDIKITVTT NELIAWSMNE TDTTLCQVR FQKSFFEEYE FKPHEIVFGE NGVQVIEDTY GNSHKLYSFR VNGRHLTTIS RKPDGDGIKS FTIAVNNTST C PESLANRL ...String:
MDYKDDDDKD YKDDDDKDYK DDDDKLEVLF QGPGMSFKAT ITESGKQNIW FRAIYVLSTI QDDIKITVTT NELIAWSMNE TDTTLCQVR FQKSFFEEYE FKPHEIVFGE NGVQVIEDTY GNSHKLYSFR VNGRHLTTIS RKPDGDGIKS FTIAVNNTST C PESLANRL IVVIEMDSLI VKEYCPQFQP IKYDPIIINL KYKRRFLDVF GTAASDRNPQ EPLDPKLLDV FTNTERELTS AL FNEEVES DIRKRNQLTA ADEINYICCN STLLKNFLDN CNVNVTDEVK LEINVHRLSI TAFTKAVYGK NNDLLRNALS MSN TISTLD LEHYCLFTTI EDEKQDKRSH SKRREHMKSI IFKLKDFKNF ITIGPSWKTT QDGNDNISLW FCHPGDPILM QMQK PGVKL ELVEVTDSNI NDDILEGKFI KTAISGSKEE AGLKDNKESC ESPLKSKTAL KRENLPHSVA GTRNSPLKVS YLTPD NGST VAKTYRNNTA RKLFVEEQSQ STNYEQDKRF RQASSVHMNM NREQSFDIGT THEVACPRNE SNSLKRSIAD ICNETE DPT QQSTFAKRAD TTVTWGKALP AADDEVSCSN IDRKGMLKKE KLKHMQGLLN SQNDTSNHKK QDNKEMEDGL GLTQVEK PR GIFD

UniProtKB: DDC1 isoform 1

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Macromolecule #7: DNA damage checkpoint control protein MEC3

MacromoleculeName: DNA damage checkpoint control protein MEC3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 53.207797 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKLKLIVNGC EAPDDYKLLR TTINTVASLR KTAILRFNSE RLTIISTPKS SLNSSNNGTI LRGDTGQLWC TIPHDVFRLY TVISARELN TITMECNCDS LLSVFKRYDR VMNQGSSSNM TIKLQSMPEW NTNNGTLSGG TAGGVDTTSK PNPICALGIT F EEIVHTSG ...String:
MKLKLIVNGC EAPDDYKLLR TTINTVASLR KTAILRFNSE RLTIISTPKS SLNSSNNGTI LRGDTGQLWC TIPHDVFRLY TVISARELN TITMECNCDS LLSVFKRYDR VMNQGSSSNM TIKLQSMPEW NTNNGTLSGG TAGGVDTTSK PNPICALGIT F EEIVHTSG PNDAIVMNGG VDEHNGLPTT VGTGNLLASN KVIMHSFKVP VKLLFRAQDT RIQEPMINYI QLMMYKLPPI SG EFGSAFH GFIRRVERYS NVNHIHLMGV KKKEHGNEGD DVELKIIVNE LDWHLEICWN GPLDSVIQRQ EGLTDNPSQN QHI DTDGRQ EEGSLPIIEA DKPMSSLYTN TRDREMEENI RYDEDLLRIE DSSIADTRGN IYTADTSGDT EFNDISVMVE KAEQ ESSST HEVIIRCKDW KVCSKLYAAF EEVVLAISHD ESCVFHCSLD RGSLEDSEDV EKPRERGQII YYIARSKGL

UniProtKB: DNA damage checkpoint control protein MEC3

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Macromolecule #8: RAD24 isoform 1

MacromoleculeName: RAD24 isoform 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 80.096828 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDSTNLNKRP LLQYSLSSLG SQITKWSSSR PTSPVRKARS TENDFLSKQD TSSILPSIND DGGEQWYEKF KPNCLEQVAI HKRKLKDVQ EALDAMFLPN AKHRILLLSG PSGCSKSTVI KELSKILVPK YRQNSNGTSF RSTPNEHKVT EFRGDCIVND L PQMESFSE ...String:
MDSTNLNKRP LLQYSLSSLG SQITKWSSSR PTSPVRKARS TENDFLSKQD TSSILPSIND DGGEQWYEKF KPNCLEQVAI HKRKLKDVQ EALDAMFLPN AKHRILLLSG PSGCSKSTVI KELSKILVPK YRQNSNGTSF RSTPNEHKVT EFRGDCIVND L PQMESFSE FLKGARYLVM SNLSLILIED LPNVFHIDTR RRFQQLILQW LYSSEPLLPP LVICITECEI PENDNNYRKF GI DYTFSAE TIMNKEILMH PRLKRIKFNP INSTLLKKHL KFICVQNMKM LKEKNKWNKR QEVIDYIAQE TGDIRSAITT LQF WATSSG SLPISTREST ISYFHAIGKV IHGSHSTNND NEMINNLFEN SNNLLSKEDF KLGILENYNT FNKGEFSISD ASSI VDCLS ECDNMNGLPE SNEYGLREVR KTFRNISKQG HNHGTVYFPR EWKVRKLQNS FKVQAEDWLN VSLYKYNAVH SFRNI TLEF GYYAPLIRKC QSYKKKYILY YLKNLPSGSS GPKQTMDKFS DIMKVENGID VVDRIGGPIE ALSVEDGLAP LMDNDS NNC DHLEDQKKER DRRLRMLIDQ YERNVMMAND DLEDEETSFN DDPIVDSDSD NSNNIGNETF GRSDEDESLC EILSQRQ PR KAPVISESLS DSDLEILGLN LEVLFQGPGG DYKDDDDKDY KDDDDKDYKD DDDK

UniProtKB: RAD24 isoform 1

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Macromolecule #9: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.507701 KDa
SequenceString: (DG)(DG)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA) (DG)(DG)(DA)(DA)(DG)(DG)(DA)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String:
(DG)(DG)(DA)(DC)(DG)(DA)(DG)(DT)(DC)(DA) (DG)(DG)(DA)(DA)(DG)(DG)(DA)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #10: DNA (5'-D(P*CP*GP*TP*CP*CP*CP*TP*TP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*CP*GP*TP*CP*CP*CP*TP*TP*CP*C)-3') / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 5.972841 KDa
SequenceString:
(DC)(DG)(DC)(DT)(DC)(DC)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DC)(DT)(DC)(DG)(DT)(DC)(DC)

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #12: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 12 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #13: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 429 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
25.0 mMHEPES-KOH
300.0 mMpotassium acetate
7.0 mMmagnesium acetate
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 938420
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7st9


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8dqw:
Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction

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