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- EMDB-14527: Structure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 che... -

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Basic information

Entry
Database: EMDB / ID: EMD-14527
TitleStructure of DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
Map dataMap
Sample
  • Complex: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
    • Protein or peptide: Cell cycle checkpoint control protein RAD9A
    • Protein or peptide: Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17
    • Protein or peptide: Checkpoint protein HUS1
    • 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
    • DNA: Hairpin DNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsDNA damage checkpoint / Rad17-RFC / 9-1-1 / DNA BINDING PROTEIN
Function / homology
Function and homology information


meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA clamp loader activity ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / Rad17 RFC-like complex / Elg1 RFC-like complex / DNA replication factor C complex / Ctf18 RFC-like complex / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA clamp loader activity / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / DNA replication checkpoint signaling / regulation of phosphorylation / embryo development ending in birth or egg hatching / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein localization to site of double-strand break / Polymerase switching on the C-strand of the telomere / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / Impaired BRCA2 binding to RAD51 / negative regulation of DNA replication / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / ATP-dependent activity, acting on DNA / Activation of ATR in response to replication stress / response to UV / 3'-5' exonuclease activity / substantia nigra development / telomere maintenance / Translesion synthesis by REV1 / DNA damage checkpoint signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / cellular response to ionizing radiation / nucleotide-excision repair / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / SH3 domain binding / Dual Incision in GG-NER / DNA-templated DNA replication / histone deacetylase binding / intrinsic apoptotic signaling pathway in response to DNA damage / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / DNA replication / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / protein kinase binding / nucleolus / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / Rad17 P-loop domain / Checkpoint protein Hus1/Mec3 / Hus1-like protein / Checkpoint protein Rad17/Rad24 / Checkpoint protein Rad17/Rad24, fungi/metazoa / Rad1/Rec1/Rad17 ...Cell cycle checkpoint protein, Rad1 / Cell cycle checkpoint, Hus1 / Rad9 / Rad9 / 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 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
Cell cycle checkpoint protein RAD1 / Checkpoint protein HUS1 / Cell cycle checkpoint protein RAD17 / Replication factor C subunit 4 / Replication factor C subunit 2 / Replication factor C subunit 5 / Replication factor C subunit 3 / Cell cycle checkpoint control protein RAD9A
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsDay M / Oliver AW / Pearl LH
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
Cancer Research UKC302/A24386 United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction.
Authors: Matthew Day / Antony W Oliver / Laurence H Pearl /
Abstract: The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or ...The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5'-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5' DNA end and fixes the orientation of 9-1-1 on the ssDNA.
History
DepositionMar 11, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14527.png

Downloads & links

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Map

FileDownload / File: emd_14527.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 296 pix.
= 254.56 Å		0.86 Å/pix.
x 296 pix.
= 254.56 Å		0.86 Å/pix.
x 296 pix.
= 254.56 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.0019020431 - 2.0835643
Average (Standard dev.)0.0029825892 (±0.038953133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 254.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_14527_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_14527_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp

EntireName: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
Components
  • Complex: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
    • Protein or peptide: Cell cycle checkpoint control protein RAD9A
    • Protein or peptide: Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17
    • Protein or peptide: Checkpoint protein HUS1
    • 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
    • DNA: Hairpin DNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp

SupramoleculeName: DNA-bound human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Cell cycle checkpoint control protein RAD9A

MacromoleculeName: Cell cycle checkpoint control protein RAD9A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease III
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.260023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKCLVTGGNV KVLGKAVHSL SRIGDELYLE PLEDGLSLRT VNSSRSAYAC FLFAPLFFQQ YQAATPGQDL LRCKILMKSF LSVFRSLAM LEKTVEKCCI SLNGRSSRLV VQLHCKFGVR KTHNLSFQDC ESLQAVFDPA SCPHMLRAPA RVLGEAVLPF S PALAEVTL ...String:
MKCLVTGGNV KVLGKAVHSL SRIGDELYLE PLEDGLSLRT VNSSRSAYAC FLFAPLFFQQ YQAATPGQDL LRCKILMKSF LSVFRSLAM LEKTVEKCCI SLNGRSSRLV VQLHCKFGVR KTHNLSFQDC ESLQAVFDPA SCPHMLRAPA RVLGEAVLPF S PALAEVTL GIGRGRRVIL RSYHEEEADS TAKAMVTEMC LGEEDFQQLQ AQEGVAITFC LKEFRGLLSF AESANLNLSI HF DAPGRPA IFTIKDSLLD GHFVLATLSD TDSHSQDLGS PERHQPVPQL QAHSTPHPDD FANDDIDSYM IAMETTIGNE GSR VLPSIS LSPGPQPPKS PGPHSEEEDE AEPSTVPGTP PPKKFRSLFF GSILAPVRSP QGPSPVLAED SEGEGTSAGS RHHH HHHHH

UniProtKB: Cell cycle checkpoint control protein RAD9A

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Macromolecule #2: Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17

MacromoleculeName: Cell cycle checkpoint protein RAD1,Cell cycle checkpoint protein RAD17
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: exodeoxyribonuclease III
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 115.195578 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPLLTQQIQD EDDQYSLVAS LDNVRNLSTI LKAIHFREHA TCFATKNGIK VTVENAKCVQ ANAFIQAGIF QEFKVQEESV TFRINLTVL LDCLSIFGSS PMPGTLTALR MCYQGYGYPL MLFLEEGGVV TVCKINTQEP EETLDFDFCS TNVINKIILQ S EGLREAFS ...String:
MPLLTQQIQD EDDQYSLVAS LDNVRNLSTI LKAIHFREHA TCFATKNGIK VTVENAKCVQ ANAFIQAGIF QEFKVQEESV TFRINLTVL LDCLSIFGSS PMPGTLTALR MCYQGYGYPL MLFLEEGGVV TVCKINTQEP EETLDFDFCS TNVINKIILQ S EGLREAFS ELDMTSEVLQ ITMSPDKPYF RLSTFGNAGS SHLDYPKDSD LMEAFHCNQT QVNRYKISLL KPSTKALVLS CK VSIRTDN RGFLSLQYMI RNEDGQICFV EYYCCPDEEV PESESGRGSM SAWSHPQFEK GSAGSAAGSG AGWSHPQFEK LEV LFQGPG HMSKTFLRPK VSSTKVTDWV DPSFDDFLEC SGVSTITATS LGVNNSSHRR KNGPSTLESS RFPARKRGNL SSLE QIYGL ENSKEYLSEN EPWVDKYKPE TQHELAVHKK KIEEVETWLK AQVLERQPKQ GGSILLITGP PGCGKTTTLK ILSKE HGIQ VQEWINPVLP DFQKDDFKGM FNTESSFHMF PYQSQIAVFK EFLLRATKYN KLQMLGDDLR TDKKIILVED LPNQFY RDS HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM KFLNRIVTIE ANKNGGK IT VPDKTSLELL CQGCSGDIRS AINSLQFSSS KGENNLRPRK KGMSLKSDAV LSKSKRRKKP DRVFENQEVQ AIGGKDVS L FLFRALGKIL YCKRASLTEL DSPRLPSHLS EYERDTLLVE PEEVVEMSHM PGDLFNLYLH QNYIDFFMEI DDIVRASEF LSFADILSGD WNTRSLLREY STSIATRGVM HSNKARGYAH CQGGGSSFRP LHKPQWFLIN KKYRENCLAA KALFPDFCLP ALCLQTQLL PYLALLTIPM RNQAQISFIQ DIGRLPLKRH FGRLKMEALT DREHGMIDPD SGDEAQLNGG HSAEESLGEP T QATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI IIEDYESDGT LEGASHHHHH HHH

UniProtKB: Cell cycle checkpoint protein RAD1, Cell cycle checkpoint protein RAD17

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Macromolecule #3: Checkpoint protein HUS1

MacromoleculeName: Checkpoint protein HUS1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.731854 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKFRAKIVDG ACLNHFTRIS NMIAKLAKTC TLRISPDKLN FILCDKLANG GVSMWCELEQ ENFFNEFQME GVSAENNEIY LELTSENLS RALKTAQNAR ALKIKLTNKH FPCLTVSVEL LSMSSSSRIV THDIPIKVIP RKLWKDLQEP VVPDPDVSIY L PVLKTMKS ...String:
MKFRAKIVDG ACLNHFTRIS NMIAKLAKTC TLRISPDKLN FILCDKLANG GVSMWCELEQ ENFFNEFQME GVSAENNEIY LELTSENLS RALKTAQNAR ALKIKLTNKH FPCLTVSVEL LSMSSSSRIV THDIPIKVIP RKLWKDLQEP VVPDPDVSIY L PVLKTMKS VVEKMKNISN HLVIEANLDG ELNLKIETEL VCVTTHFKDL GNPPLASEST HEDRNVEHMA EVHIDIRKLL QF LAGQQVN PTKALCNIVN NKMVHFDLLH EDVSLQYFIP ALS

UniProtKB: Checkpoint protein HUS1

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Macromolecule #4: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.719648 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME ...String:
MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME KESKTTRFCL ICNYVSRIIE PLTSRCSKFR FKPLSDKIQQ QRLLDIAKKE NVKISDEGIA YLVKVSEGDL RK AITFLQS ATRLTGGKEI TEKVITDIAG VIPAEKIDGV FAACQSGSFD KLEAVVKDLI DEGHAATQLV NQLHDVVVEN NLS DKQKSI ITEKLAEVDK CLADGADEHL QLISLCATVM QQLSQNS

UniProtKB: Replication factor C subunit 4

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Macromolecule #5: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.614332 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST ...String:
MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST SKVIPPIRSR CLAVRVPAPS IEDICHVLST VCKKEGLNLP SQLAHRLAEK SCRNLRKALL MCEACRVQQY PF TADQEIP ETDWEVYLRE TANAIVSQQT PQRLLEVRGR LYELLTHCIP PEIIMKGLLS ELLHNCDGQL KGEVAQMAAY YEH RLQLGS KAIYHLEAFV AKFMALYKKF MEDGLEGMMF

UniProtKB: Replication factor C subunit 3

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Macromolecule #6: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.203207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA ...String:
MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA LACNASDKII EPIQSRCAVL RYTKLTDAQI LTRLMNVIEK ERVPYTDDGL EAIIFTAQGD MRQALNNLQS TF SGFGFIN SENVFKVCDE PHPLLVKEMI QHCVNANIDE AYKILAHLWH LGYSPEDIIG NIFRVCKTFQ MAEYLKLEFI KEI GYTHMK IAEGVNSLLQ MAGLLARLCQ KTMAPVAS

UniProtKB: Replication factor C subunit 2

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Macromolecule #7: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.688816 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSHHHHHHS AALEVLFQGP GETSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTST ILACAKQLYK DKEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR R VIEKFTEN ...String:
MGSHHHHHHS AALEVLFQGP GETSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTST ILACAKQLYK DKEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR R VIEKFTEN TRFCLICNYL SKIIPALQSR CTRFRFGPLT PELMVPRLEH VVEEEKVDIS EDGMKALVTL SSGDMRRALN IL QSTNMAF GKVTEETVYT CTGHPLKSDI ANILDWMLNQ DFTTAYRNIT ELKTLKGLAL HDILTEIHLF VHRVDFPSSV RIH LLTKMA DIEYRLSVGT NEKIQLSSLI AAFQVTRDLI VAEA

UniProtKB: Replication factor C subunit 5

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Macromolecule #8: Hairpin DNA

MacromoleculeName: Hairpin DNA / type: dna / ID: 8
Details: DNA with the sequence CCCGTATATTCTCCTACAGCACTAAATAATAGTGCTGTAGGAGAATATACGGGCTGCTCGTGTTGACAAGTACTGAT which forms a hairpin DNA molecule with 24 base-pairs of fully-complementary dsDNA capped ...Details: DNA with the sequence CCCGTATATTCTCCTACAGCACTAAATAATAGTGCTGTAGGAGAATATACGGGCTGCTCGTGTTGACAAGTACTGAT which forms a hairpin DNA molecule with 24 base-pairs of fully-complementary dsDNA capped with a tetraloop at one end, and with a 24 nucleotide 3' overhang
Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.761232 KDa
SequenceString: (DC)(DC)(DC)(DG)(DT)(DA)(DT)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DT)(DA)(DC)(DA)(DG)(DC) (DA)(DC)(DT)(DA)(DA)(DA)(DT)(DA)(DA) (DT)(DA)(DG)(DT)(DG)(DC)(DT)(DG)(DT)(DA) (DG) (DG)(DA)(DG)(DA)(DA)(DT) ...String:
(DC)(DC)(DC)(DG)(DT)(DA)(DT)(DA)(DT)(DT) (DC)(DT)(DC)(DC)(DT)(DA)(DC)(DA)(DG)(DC) (DA)(DC)(DT)(DA)(DA)(DA)(DT)(DA)(DA) (DT)(DA)(DG)(DT)(DG)(DC)(DT)(DG)(DT)(DA) (DG) (DG)(DA)(DG)(DA)(DA)(DT)(DA)(DT) (DA)(DC)(DG)(DG)(DG)(DC)(DT)(DG)(DC)(DT) (DC)(DG) (DT)(DG)(DT)(DT)(DG)(DA)(DC) (DA)(DA)(DG)(DT)(DA)(DC)(DT)(DG)(DA)(DT)

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Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 5 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.21 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 34.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150626
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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