3JC5 | pdb_00003jc5

Structure of the eukaryotic replicative CMG helicase and pumpjack motion


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Structure of the eukaryotic replicative CMG helicase suggests a pumpjack motion for translocation.

Yuan, Z.Bai, L.Sun, J.Georgescu, R.Liu, J.O'Donnell, M.E.Li, H.

(2016) Nat Struct Mol Biol 23: 217-224

  • DOI: https://doi.org/10.1038/nsmb.3170
  • Primary Citation Related Structures: 
    3JC5, 3JC6, 3JC7

  • PubMed Abstract: 

    The CMG helicase is composed of Cdc45, Mcm2-7 and GINS. Here we report the structure of the Saccharomyces cerevisiae CMG, determined by cryo-EM at a resolution of 3.7-4.8 Å. The structure reveals that GINS and Cdc45 scaffold the N tier of the helicase while enabling motion of the AAA+ C tier. CMG exists in two alternating conformations, compact and extended, thus suggesting that the helicase moves like an inchworm. The N-terminal regions of Mcm2-7, braced by Cdc45-GINS, form a rigid platform upon which the AAA+ C domains make longitudinal motions, nodding up and down like an oil-rig pumpjack attached to a stable platform. The Mcm ring is remodeled in CMG relative to the inactive Mcm2-7 double hexamer. The Mcm5 winged-helix domain is inserted into the central channel, thus blocking entry of double-stranded DNA and supporting a steric-exclusion DNA-unwinding model.


  • Organizational Affiliation
    • Department of Biochemistry &Cell Biology, Stony Brook University, Stony Brook, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 785.76 kDa 
  • Atom Count: 40,041 
  • Modeled Residue Count: 5,039 
  • Deposited Residue Count: 6,968 
  • Unique protein chains: 11

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 45G [auth c]650Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5H [auth D]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2I [auth B]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2YJL072CHRF213J1086
UniProt
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1J [auth A]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1YDR013WPZA208YD8119.18
UniProt
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3K [auth C]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3YOL146W
UniProt
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2016-03-16
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Data processing, Structure summary
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2024-11-27
    Changes: Data collection, Database references, Refinement description, Structure summary