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- PDB-6raz: D. melanogaster CMG-DNA, State 2B -

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Entry
Database: PDB / ID: 6raz
TitleD. melanogaster CMG-DNA, State 2B
Components
  • (DNA replication licensing factor ...) x 6
  • (DNA) x 2
  • AT18545p
  • CDC45L
  • DNA replication complex GINS protein SLD5
  • IP07275p
  • Probable DNA replication complex GINS protein PSF2
KeywordsHYDROLASE / Helicase / ATPase / AAA+ / DNA unwinding
Function / homology
Function and homology information


Unwinding of DNA / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA endoreduplication / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / DNA strand elongation involved in mitotic DNA replication ...Unwinding of DNA / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA endoreduplication / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / resolution of meiotic recombination intermediates / premeiotic DNA replication / mitotic DNA replication / CMG complex / DNA replication preinitiation complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / chromosome condensation / DNA strand elongation involved in DNA replication / DNA replication origin binding / DNA replication initiation / DNA helicase activity / regulation of DNA-templated transcription elongation / mitotic spindle organization / meiotic cell cycle / helicase activity / mitotic cell cycle / single-stranded DNA binding / DNA helicase / DNA replication / cell division / chromatin binding / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DNA replication licensing factor MCM2-like, winged-helix domain / : / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 ...DNA replication licensing factor MCM2-like, winged-helix domain / : / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / 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 / GINS, helical bundle-like domain superfamily / : / 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 domain profile. / minichromosome maintenance proteins / MCM domain / 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 / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / CDC45L / DNA replication licensing factor Mcm2 / DNA replication licensing factor MCM4 / DNA replication licensing factor Mcm6 / DNA replication complex GINS protein SLD5 / DNA replication licensing factor Mcm5 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / CDC45L / DNA replication licensing factor Mcm2 / DNA replication licensing factor MCM4 / DNA replication licensing factor Mcm6 / DNA replication complex GINS protein SLD5 / DNA replication licensing factor Mcm5 / Probable DNA replication complex GINS protein PSF2 / DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein PSF3 / DNA replication licensing factor Mcm7 / DNA replication licensing factor Mcm3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsEickhoff, P. / Martino, F. / Costa, A.
CitationJournal: Cell Rep / Year: 2019
Title: Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome.
Authors: Patrik Eickhoff / Hazal B Kose / Fabrizio Martino / Tatjana Petojevic / Ferdos Abid Ali / Julia Locke / Nele Tamberg / Andrea Nans / James M Berger / Michael R Botchan / Hasan Yardimci / Alessandro Costa /
Abstract: In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single- ...In the eukaryotic replisome, DNA unwinding by the Cdc45-MCM-Go-Ichi-Ni-San (GINS) (CMG) helicase requires a hexameric ring-shaped ATPase named minichromosome maintenance (MCM), which spools single-stranded DNA through its central channel. Not all six ATPase sites are required for unwinding; however, the helicase mechanism is unknown. We imaged ATP-hydrolysis-driven translocation of the CMG using cryo-electron microscopy (cryo-EM) and found that the six MCM subunits engage DNA using four neighboring protomers at a time, with ATP binding promoting DNA engagement. Morphing between different helicase states leads us to suggest a non-symmetric hand-over-hand rotary mechanism, explaining the asymmetric requirements of ATPase function around the MCM ring of the CMG. By imaging of a higher-order replisome assembly, we find that the Mrc1-Csm3-Tof1 fork-stabilization complex strengthens the interaction between parental duplex DNA and the CMG at the fork, which might support the coupling between DNA translocation and fork unwinding.
History
DepositionApr 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 18, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 18, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Jan 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.type / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id
Revision 2.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Revision 2.2Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_admin / ndb_struct_na_base_pair ...em_admin / ndb_struct_na_base_pair / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
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Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
X: DNA
Y: DNA
A: CDC45L
H: IP07275p
L: Probable DNA replication complex GINS protein PSF2
M: AT18545p
N: DNA replication complex GINS protein SLD5
2: DNA replication licensing factor Mcm2
5: DNA replication licensing factor Mcm5
6: DNA replication licensing factor Mcm6
3: DNA replication licensing factor Mcm3
4: DNA replication licensing factor MCM4
7: DNA replication licensing factor Mcm7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)717,82819
Polymers714,94513
Non-polymers2,8836
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area58210 Å2
ΔGint-246 kcal/mol
Surface area258690 Å2
MethodPISA

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Components

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DNA chain , 2 types, 2 molecules XY

#1: DNA chain DNA


Mass: 6389.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#2: DNA chain DNA


Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)

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Protein , 5 types, 5 molecules AHLMN

#3: Protein CDC45L / EG:BACR7A4.11 protein / LD35753p


Mass: 65968.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: CDC45L, anon-1Ec, CDC45, Cdc45, cdc45, D, dCDC45, dCDC45L, DmCdc45, Dmel\CG3658, EG:BACR7A4.11, CG3658, Dmel_CG3658
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O96989
#4: Protein IP07275p / Psf1


Mass: 23333.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Psf1, CG9187-PA, Dmel\CG9187, psf1, CG9187, Dmel_CG9187
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W0I7
#5: Protein Probable DNA replication complex GINS protein PSF2 / GINS complex subunit 2


Mass: 23141.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Psf2, CG18013 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VQY9
#6: Protein AT18545p / CG2222-PA / Psf3 / isoform A / isoform B / isoform C


Mass: 24829.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Psf3, Dmel\CG2222, CG2222, Dmel_CG2222 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W2V7
#7: Protein DNA replication complex GINS protein SLD5


Mass: 26148.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Sld5, anon-WO0172774.61, Dmel\CG14549, CG14549, Dmel_CG14549
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VBI1

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DNA replication licensing factor ... , 6 types, 6 molecules 256347

#8: Protein DNA replication licensing factor Mcm2 / Minichromosome maintenance 2 protein / DmMCM2


Mass: 100537.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm2, CG7538 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49735, DNA helicase
#9: Protein DNA replication licensing factor Mcm5 / Minichromosome maintenance 5 protein / DmMCM5


Mass: 82375.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm5, CG4082 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9VGW6, DNA helicase
#10: Protein DNA replication licensing factor Mcm6 / DmMCM6


Mass: 92467.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm6, CG4039 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9V461, DNA helicase
#11: Protein DNA replication licensing factor Mcm3 / Minichromosome maintenance 3 protein / DmMCM3


Mass: 91045.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm3, Mcm3-RA, CG4206 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XYU1, DNA helicase
#12: Protein DNA replication licensing factor MCM4 / Protein disc proliferation abnormal


Mass: 96735.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dpa, CG1616 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q26454, DNA helicase
#13: Protein DNA replication licensing factor Mcm7 / Minichromosome maintenance 7 protein / DmMCM3


Mass: 81399.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mcm7, CG4978 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9XYU0, DNA helicase

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Non-polymers , 2 types, 6 molecules

#14: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#15: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1CMG helicase bound to forked DNA in the presence of ATP, State 2BCOMPLEX#1-#130MULTIPLE SOURCES
2CMG helicaseCOMPLEX#3-#131RECOMBINANT
3DNACOMPLEX#1-#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Drosophila melanogaster (fruit fly)7227
33Drosophila melanogaster (fruit fly)7227
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33synthetic construct (others)32630
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61082 / Symmetry type: POINT

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