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- PDB-9rhi: pre-Initiation Complex on ARS1 DNA (monomer) -

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Basic information

Entry
Database: PDB / ID: 9rhi
Titlepre-Initiation Complex on ARS1 DNA (monomer)
Components
  • (DNA (31-MER)) x 2
  • (DNA replication complex GINS protein ...) x 4
  • (DNA replication licensing factor ...) x 5
  • (DNA replication regulator ...) x 2
  • Cell division control protein 45
  • DNA polymerase epsilon subunit B
  • Minichromosome maintenance protein 5
  • Mitochondrial morphogenesis protein SLD7
KeywordsREPLICATION / Macromolecular Complex DNA ATPase Helicase MCM2-7
Function / homology
Function and homology information


regulation of mitotic DNA replication initiation / mating type switching / DNA-templated DNA replication maintenance of fidelity / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state ...regulation of mitotic DNA replication initiation / mating type switching / DNA-templated DNA replication maintenance of fidelity / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / GINS complex / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / mitotic DNA replication / DNA replication checkpoint signaling / nuclear pre-replicative complex / CMG complex / : / DNA replication preinitiation complex / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / MCM complex / mitotic DNA replication initiation / silent mating-type cassette heterochromatin formation / single-stranded DNA helicase activity / recombinational repair / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / mitotic G2 DNA damage checkpoint signaling / nuclear replication fork / Dual incision in TC-NER / DNA replication origin binding / chromosome, centromeric region / error-prone translesion synthesis / DNA replication initiation / protein kinase activator activity / subtelomeric heterochromatin formation / DNA polymerase binding / replication fork / DNA helicase activity / helicase activity / transcription elongation by RNA polymerase II / DNA-templated DNA replication / spindle pole / peroxisome / nuclear envelope / heterochromatin formation / single-stranded DNA binding / DNA helicase / chromosome, telomeric region / DNA replication / DNA damage response / chromatin binding / chromatin / endoplasmic reticulum / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Mitochondrial morphogenesis protein Sld7 / Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain ...Mitochondrial morphogenesis protein Sld7 / Sld7 C-terminal domain / Sld7, N-terminal / Sld7 C-terminal domain / Mitochondrial morphogenesis protein SLD7 N-terminal domain / Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / DNA polymerase epsilon, subunit B / : / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / DNA replication complex GINS protein Psf2 / CDC45 family / CDC45 / GINS complex, subunit Psf3 / DNA replication complex GINS protein SLD5, C-terminal / GINS complex, subunit Psf3 superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / GINS complex, subunit Psf1 / : / MCM3 winged helix domain / GINS, helical bundle-like domain superfamily / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / BRCT domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family C-terminal AAA(+) ATPase domain (MCM-CTD) profile. / minichromosome maintenance proteins / MCM domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA replication licensing factor MCM3 / DNA polymerase epsilon subunit B / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication complex GINS protein PSF2 ...ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA replication licensing factor MCM3 / DNA polymerase epsilon subunit B / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication complex GINS protein PSF2 / DNA replication regulator DPB11 / DNA replication licensing factor MCM6 / DNA replication regulator SLD3 / DNA replication complex GINS protein SLD5 / Cell division control protein 45 / Mitochondrial morphogenesis protein SLD7 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPuehringer, T. / Butryn, A. / Couves, E.C. / Costa, A.
Funding support United Kingdom, European Union, Germany, 4items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001065 United Kingdom
The Francis Crick InstituteFC001066 United Kingdom
European Research Council (ERC)820102European Union
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: To Be Published
Title: Structure of the pre-initiation complex explains CMG biogenesis
Authors: Puehringer, T. / Canal, B. / Palm, G. / Butryn, A. / Couves, E.C. / Willhoft, O. / Lewis, J.S. / Diffley, J.F.X. / Costa, A.
History
DepositionJun 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: Minichromosome maintenance protein 5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
A: DNA (31-MER)
B: DNA (31-MER)
C: DNA replication complex GINS protein PSF3
D: DNA replication complex GINS protein SLD5
E: Cell division control protein 45
F: DNA polymerase epsilon subunit B
H: DNA replication complex GINS protein PSF1
I: DNA replication complex GINS protein PSF2
Q: DNA replication regulator SLD3
R: Mitochondrial morphogenesis protein SLD7
S: DNA replication regulator DPB11
T: DNA replication regulator SLD3
f: DNA replication licensing factor MCM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,270,28226
Polymers1,269,50419
Non-polymers7797
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA replication licensing factor ... , 5 types, 6 molecules 23467f

#1: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2


Mass: 98911.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM2, YBL023C, YBL0438 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29469, DNA helicase
#2: Protein DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 111720.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal CBP-tag with TEV protease cleavage site in frame with MCM3
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM3, YEL032W, SYGP-ORF23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24279, DNA helicase
#3: Protein DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM4, CDC54, HCD21, YPR019W, YP9531.13 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30665, DNA helicase
#5: Protein DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM6, YGL201C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53091, DNA helicase
#6: Protein DNA replication licensing factor MCM7 / Cell division control protein 47 / Minichromosome maintenance protein 7


Mass: 95049.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM7, CDC47, YBR202W, YBR1441 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38132, DNA helicase

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Protein , 4 types, 4 molecules 5EFR

#4: Protein Minichromosome maintenance protein 5 / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MCM5, CDC46, YLR274W, L9328.1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29496, DNA helicase
#11: Protein Cell division control protein 45


Mass: 75154.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal ...Details: Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag,Internal 2xFLAG tag
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC45, SLD4, YLR103C, L8004.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08032
#12: Protein DNA polymerase epsilon subunit B / DNA polymerase II subunit 2


Mass: 78425.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DPB2, YPR175W, P9705.7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24482
#16: Protein Mitochondrial morphogenesis protein SLD7 / Synthetic lethality with DPB11-24 mutation protein 7


Mass: 29598.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLD7, YOR060C, YOR29-11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08457

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DNA chain , 2 types, 2 molecules AB

#7: DNA chain DNA (31-MER)


Mass: 9512.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#8: DNA chain DNA (31-MER)


Mass: 9547.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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DNA replication complex GINS protein ... , 4 types, 4 molecules CDHI

#9: Protein DNA replication complex GINS protein PSF3 / Partner of Sld five 3


Mass: 24437.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PSF3, YOL146W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12146
#10: Protein DNA replication complex GINS protein SLD5


Mass: 33983.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLD5, YDR489W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03406
#13: Protein DNA replication complex GINS protein PSF1 / Partner of Sld five 1


Mass: 24230.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PSF1, YDR013W, PZA208, YD8119.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12488
#14: Protein DNA replication complex GINS protein PSF2 / Partner of Sld five 2


Mass: 25096.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PSF2, YJL072C, HRF213, J1086 / Production host: Escherichia coli (E. coli) / References: UniProt: P40359

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DNA replication regulator ... , 2 types, 3 molecules QTS

#15: Protein DNA replication regulator SLD3


Mass: 81240.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Yeast Sld3 in frame with C-terminal TEV protease cleavage site and Twin-Strep-Tag
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLD3, YGL113W, G2980 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53135
#17: Protein DNA replication regulator DPB11


Mass: 91548.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Yeast Dpb11 in frame with C-terminal 3C protease cleavage site and 3xFLAG tag
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DPB11, YJL090C, J0918 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47027

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Non-polymers , 3 types, 7 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#19: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#20: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pre-initiation complex (Monomer) on replication origin (DNA)
Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 59347

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3PHENIX1.21_5207model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1572464
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 302350 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 182.83 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002146834
ELECTRON MICROSCOPYf_angle_d0.479863505
ELECTRON MICROSCOPYf_chiral_restr0.047332
ELECTRON MICROSCOPYf_plane_restr0.00347882
ELECTRON MICROSCOPYf_dihedral_angle_d11.5326760

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