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 6RAY | pdb_00006ray

D. melanogaster CMG-DNA, State 2A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Molecular Basis for ATP-Hydrolysis-Driven DNA Translocation by the CMG Helicase of the Eukaryotic Replisome.

Eickhoff, P., Kose, H.B., Martino, F., Petojevic, T., Abid Ali, F., Locke, J., Tamberg, N., Nans, A., Berger, J.M., Botchan, M.R., Yardimci, H., Costa, A.

(2019) Cell Rep 28: 2673-2688.e8

  • DOI: https://doi.org/10.1016/j.celrep.2019.07.104
  • Primary Citation Related Structures: 
    6RAW, 6RAX, 6RAY, 6RAZ

  • PubMed 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-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.


  • Organizational Affiliation: 
    • Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.

Macromolecule Content 

  • Total Structure Weight: 714.78 kDa 
  • Atom Count: 39,071 
  • Modeled Residue Count: 4,900 
  • Deposited Residue Count: 6,275 
  • Unique protein chains: 11
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor Mcm3A [auth 3]819Drosophila melanogasterMutation(s): 0 
Gene Names: Mcm3, Mcm3-RA, CG4206
EC: 3.6.4.12
UniProt
Find proteins for Q9XYU1 (Drosophila melanogaster)
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UniProt GroupQ9XYU1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4B [auth 4]866Drosophila melanogasterMutation(s): 0 
Gene Names: dpa, CG1616
EC: 3.6.4.12
UniProt
Find proteins for Q26454 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor Mcm7C [auth 7]720Drosophila melanogasterMutation(s): 0 
Gene Names: Mcm7, CG4978
EC: 3.6.4.12
UniProt
Find proteins for Q9XYU0 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor Mcm6D [auth 6]817Drosophila melanogasterMutation(s): 0 
Gene Names: Mcm6, CG4039
EC: 3.6.4.12
UniProt
Find proteins for Q9V461 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor Mcm5E [auth 5]733Drosophila melanogasterMutation(s): 0 
Gene Names: Mcm5, CG4082
EC: 3.6.4.12
UniProt
Find proteins for Q9VGW6 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
CDC45LF [auth A]575Drosophila melanogasterMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O96989 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
IP07275pG [auth H]202Drosophila melanogasterMutation(s): 0 
Gene Names: Psf1, CG9187-PA, Dmel\CG9187, psf1, CG9187, Dmel_CG9187
UniProt
Find proteins for Q9W0I7 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable DNA replication complex GINS protein PSF2H [auth L]203Drosophila melanogasterMutation(s): 0 
Gene Names: Psf2, CG18013
UniProt
Find proteins for Q9VQY9 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
AT18545pI [auth M]212Drosophila melanogasterMutation(s): 0 
Gene Names: Psf3, Dmel\CG2222, CG2222, Dmel_CG2222
UniProt
Find proteins for Q9W2V7 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth N]228Drosophila melanogasterMutation(s): 0 
Gene Names: Sld5, anon-WO0172774.61, Dmel\CG14549, CG14549, Dmel_CG14549
UniProt
Find proteins for Q9VBI1 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor Mcm2K [auth 2]887Drosophila melanogasterMutation(s): 0 
Gene Names: Mcm2, CG7538
EC: 3.6.4.12
UniProt
Find proteins for P49735 (Drosophila melanogaster)
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Reference Sequence
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')L [auth X]13Drosophila melanogaster
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary