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- EMDB-29417: EM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-29417
TitleEM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA)
Map dataEM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA)
Sample
  • Complex: Rad24-RFC-911 clamp-DNA
    • Complex: DNA
      • DNA: x 3 types
    • Complex: Proteins complexProtein
      • Protein or peptide: x 3 types
  • Protein or peptide: x 5 types
  • Ligand: x 3 types
KeywordsDNA damage repair / Rad24-RFC / 9-1-1 clamp / DNA clamp / alternative clamp loader / DNA damage signaling / DNA BINDING PROTEIN-DNA complex / CELL CYCLE-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 / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
Ddc1 / DNA damage checkpoint control protein Rad17 / Rad17 P-loop domain / 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 ...Ddc1 / DNA damage checkpoint control protein Rad17 / Rad17 P-loop domain / 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 / Checkpoint protein RAD24 / 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 speciessynthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsZheng F / Georgescu R / Yao YN / O'Donnell ME / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115809 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2023
Title: Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology.
Authors: Fengwei Zheng / Roxana E Georgescu / Nina Y Yao / Michael E O'Donnell / Huilin Li /
Abstract: Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the ...Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.
History
DepositionJan 9, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29417.png

Downloads & links

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Map

FileDownload / File: emd_29417.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of S. cerevisiae Rad24-RFC loading the 9-1-1 clamp onto a 5-nt gapped DNA (9-1-1 encircling fully bound DNA)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.7485586 - 1.2628971
Average (Standard dev.)-0.000069576374 (±0.025162054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 347.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_29417_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_29417_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 : Rad24-RFC-911 clamp-DNA

EntireName: Rad24-RFC-911 clamp-DNA
Components
  • Complex: Rad24-RFC-911 clamp-DNA
    • Complex: DNA
      • DNA: Template strandTranscription (biology)
      • DNA: Primer strand 1
      • DNA: Primer strand 2
    • Complex: Proteins complexProtein
      • Protein or peptide: DNA damage checkpoint control protein MEC3
      • Protein or peptide: DNA damage checkpoint control protein RAD17
      • Protein or peptide: DDC1 isoform 1
  • Protein or peptide: Checkpoint protein RAD24
  • Protein or peptide: Replication factor C subunit 4
  • Protein or peptide: Replication factor C subunit 3
  • Protein or peptide: Replication factor C subunit 2
  • Protein or peptide: Replication factor C subunit 5
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Rad24-RFC-911 clamp-DNA

SupramoleculeName: Rad24-RFC-911 clamp-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #6-#11

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Supramolecule #2: DNA

SupramoleculeName: DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #9-#11 / Details: synthetic DNA
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: Proteins complex

SupramoleculeName: Proteins complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Checkpoint protein RAD24

MacromoleculeName: Checkpoint protein RAD24 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 57.715633 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 QSYKK

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Macromolecule #2: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 37.841051 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

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Macromolecule #4: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: DNA damage checkpoint control protein MEC3

MacromoleculeName: DNA damage checkpoint control protein MEC3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #7: DNA damage checkpoint control protein RAD17

MacromoleculeName: DNA damage checkpoint control protein RAD17 / type: protein_or_peptide / ID: 7 / 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

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Macromolecule #8: DDC1 isoform 1

MacromoleculeName: DDC1 isoform 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 69.7875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSFKATITES GKQNIWFRAI YVLSTIQDDI KITVTTNELI AWSMNETDTT LCQVRFQKSF FEEYEFKPHE IVFGENGVQV IEDTYGNSH KLYSFRVNGR HLTTISRKPD GDGIKSFTIA VNNTSTCPES LANRLIVVIE MDSLIVKEYC PQFQPIKYDP I IINLKYKR ...String:
MSFKATITES GKQNIWFRAI YVLSTIQDDI KITVTTNELI AWSMNETDTT LCQVRFQKSF FEEYEFKPHE IVFGENGVQV IEDTYGNSH KLYSFRVNGR HLTTISRKPD GDGIKSFTIA VNNTSTCPES LANRLIVVIE MDSLIVKEYC PQFQPIKYDP I IINLKYKR RFLDVFGTAA SDRNPQEPLD PKLLDVFTNT ERELTSALFN EEVESDIRKR NQLTAADEIN YICCNSTLLK NF LDNCNVN VTDEVKLEIN VHRLSITAFT KAVYGKNNDL LRNALSMSNT ISTLDLEHYC LFTTIEDEKQ DKRSHSKRRE HMK SIIFKL KDFKNFITIG PSWKTTQDGN DNISLWFCHP GDPILMQMQK PGVKLELVEV TDSNINDDIL EGKFIKTAIS GSKE EAGLK DNKESCESPL KSKTALKREN LPHSVAGTRN SPLKVSYLTP DNGSTVAKTY RNNTARKLFV EEQSQSTNYE QDKRF RQAS SVHMNMNREQ SFDIGTTHEV ACPRNESNSL KRSIADICNE TEDPTQQSTF AKRADTTVTW GKALPAADDE VSCSNI DRK GMLKKEKLKH MQGLLNSQND TSNHKKQDNK EMEDGLGLTQ VEKPRGIFD

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Macromolecule #9: Template strand

MacromoleculeName: Template strand / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.389855 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DA)(DT)(DA)(DG)(DG)(DC) (DG)(DA)(DT)(DA)(DC)(DG)(DA)(DA)(DT)(DC) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DC)(DC)(DG)(DT)(DA)(DT)(DA)(DG)(DC) (DC) (DG)(DT)(DA)(DG)(DC)(DG)(DA)(DG) (DC)(DC)

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Macromolecule #10: Primer strand 1

MacromoleculeName: Primer strand 1 / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.150966 KDa
SequenceString:
(DG)(DG)(DC)(DT)(DC)(DG)(DC)(DT)(DA)(DC) (DG)(DG)(DC)(DT)(DA)(DT)(DA)(DC)(DG)(DG)

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Macromolecule #11: Primer strand 2

MacromoleculeName: Primer strand 2 / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.08494 KDa
SequenceString:
(DG)(DA)(DT)(DT)(DC)(DG)(DT)(DA)(DT)(DC) (DG)(DC)(DC)(DT)(DA)(DT)(DA)(DC)(DC)(DG)

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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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 13 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: 1.9000000000000001 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sgz

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242906
FSC plot (resolution estimation)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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