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- EMDB-25121: Cryo-EM 3D map of the yeast Rad24-RFC loader bound to DNA and the... -

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Basic information

Entry
Database: EMDB / ID: EMD-25121
TitleCryo-EM 3D map of the yeast Rad24-RFC loader bound to DNA and the closed 9-1-1 clamp
Map dataCryo-EM map of the yeast Rad24-RFC loader bound to the 911 clamp and DNA in a closed state
Sample
  • Complex: Rad24-RFC-911 clamp-DNA
    • Complex: dsDNA
      • DNA: x 2 types
    • Complex: Proteins
      • Protein or peptide: x 8 types
  • Ligand: x 4 types
KeywordsDNA damage repair / Rad24-RFC / 9-1-1 clamp / DNA clamp / alternative clamp loader / DNA damage signaling / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


checkpoint clamp complex / DNA clamp unloading / Rad17 RFC-like complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Elg1 RFC-like complex / Ctf18 RFC-like complex / DNA replication factor C complex / Polymerase switching / DNA clamp loader activity / nuclease activity ...checkpoint clamp complex / DNA clamp unloading / Rad17 RFC-like complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Elg1 RFC-like complex / Ctf18 RFC-like complex / DNA replication factor C complex / Polymerase switching / DNA clamp loader activity / nuclease activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / DNA replication checkpoint signaling / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / reciprocal meiotic recombination / sister chromatid cohesion / mitotic sister chromatid cohesion / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / mismatch repair / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / double-strand break repair / double-stranded DNA binding / damaged DNA binding / DNA repair / chromatin binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
DNA damage checkpoint control protein Rad17 / Rad17 P-loop domain / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Repair protein Rad1/Rec1/Rad17 / Replication factor C subunit 3, C-terminal domain / RCF1/5-like, AAA+ ATPase lid domain / Replication factor C, C-terminal / Replication factor C C-terminal domain ...DNA damage checkpoint control protein Rad17 / Rad17 P-loop domain / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 / Repair protein Rad1/Rec1/Rad17 / Replication factor C subunit 3, C-terminal domain / RCF1/5-like, AAA+ ATPase lid domain / 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
: / : / 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 RAD17
Similarity search - Component
Biological speciessynthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZheng F / Georgescu R
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: Nat Struct Mol Biol / Year: 2022
Title: DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp.
Authors: Fengwei Zheng / Roxana E Georgescu / Nina Y Yao / Michael E O'Donnell / Huilin Li /
Abstract: The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in ...The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring.
History
DepositionOct 7, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25121.png

Downloads & links

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Map

FileDownload / File: emd_25121.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the yeast Rad24-RFC loader bound to the 911 clamp and DNA in a closed state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.52843165 - 0.9579343
Average (Standard dev.)0.00033521253 (±0.018882075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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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: dsDNA
      • DNA: Watson strand
      • DNA: Crick strand
    • Complex: Proteins
      • 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
      • Protein or peptide: Mitosis Entry Checkpoint protein MEC3
      • Protein or peptide: DNA damage checkpoint control protein RAD17
      • Protein or peptide: DNA Damage Checkpoint protein DDC1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION

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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: #1-#10

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Supramolecule #2: dsDNA

SupramoleculeName: dsDNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #9-#10 / Details: synthetic DNA
Source (natural)Organism: synthetic construct (others)

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Supramolecule #3: Proteins

SupramoleculeName: Proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#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: 75.823477 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 DSDLEIL

UniProtKB: Checkpoint protein RAD24

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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

UniProtKB: Replication factor C subunit 4

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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: 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 #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

UniProtKB: Replication factor C subunit 2

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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

UniProtKB: Replication factor C subunit 5

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Macromolecule #6: Mitosis Entry Checkpoint protein MEC3

MacromoleculeName: Mitosis Entry Checkpoint protein MEC3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 51.606102 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 ERGQIIYYIA RSKGL

UniProtKB: UNIPROTKB: A0A6A5PTK1

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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

UniProtKB: DNA damage checkpoint control protein RAD17

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Macromolecule #8: DNA Damage Checkpoint protein DDC1

MacromoleculeName: DNA Damage Checkpoint protein DDC1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 67.386805 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 LFTKSIIFKL KDFKNFITIG PSW KTTQDG NDNISLWFCH PGDPILMQMQ KPGVKLELVE VTDSNINDDI LEGKFIKTAI SGSKEEAGLK DNKESCESPL KSKT ALKRE NLPHSVAGTR NSPLKVSYLT PDNGSTVAKT YRNNTARKLF VEEQSQSTNY EQDKRFRQAS SVHMNMNREQ SFDIG TTHE VACPRNESNS LKRSIADICN ETEDPTQQST FAKRADTTVT WGKALPAADD EVSCSNIDRK GMLKKEKLKH MQGLLN SQN DTSNHKKQDN KEMEDGLGLT QVEKPRGIFD

UniProtKB: UNIPROTKB: A0A7I9C529

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Macromolecule #9: Watson strand

MacromoleculeName: Watson strand / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.136008 KDa
SequenceString:
(DG)(DC)(DA)(DG)(DA)(DC)(DA)(DC)(DT)(DA) (DC)(DG)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DA)

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Macromolecule #10: Crick strand

MacromoleculeName: Crick strand / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.214818 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DA)(DC)(DT)(DC)(DG) (DT)(DA)(DG)(DT)(DG)(DT)(DC)(DT)(DG) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

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Macromolecule #11: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 11 / 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 #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #14: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147415
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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