9E2X | pdb_00009e2x

Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history. 


Literature

G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation.

Batra, S., Allwein, B., Kumar, C., Devbhandari, S., Bruning, J.G., Bahng, S., Lee, C.M., Marians, K.J., Hite, R.K., Remus, D.

(2025) Science 387: eadt1978-eadt1978

  • DOI: https://doi.org/10.1126/science.adt1978
  • Primary Citation of Related Structures:  
    9E2W, 9E2X, 9E2Y, 9E2Z

  • PubMed Abstract: 

    DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork collisions with preformed G4s in the parental DNA using reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by arresting the CMG helicase. Cryo-electron microscopy structures of stalled yeast and human CMG complexes reveal that the folded G4 is lodged inside the central CMG channel, arresting translocation. The G4 stabilizes the CMG at distinct translocation intermediates, suggesting an unprecedented helical inchworm mechanism for DNA translocation. These findings illuminate the eukaryotic replication fork mechanism under normal and perturbed conditions.

    • Organizational Affiliation: 
    • Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1208Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: PSF1, YDR013W, PZA208, YD8119.18
UniProt
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ12488
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2213Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: PSF2, YJL072C, HRF213, J1086
UniProt
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3217Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: PSF3, YOL146W
UniProt
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5294Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: SLD5, YDR489W
UniProt
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ03406
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45650Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: CDC45, SLD4, YLR103C, L8004.11
UniProt
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2H [auth 2]868Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM2, YBL023C, YBL0438
EC: 3.6.4.12
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3I [auth 3]971Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM3, YEL032W, SYGP-ORF23
EC: 3.6.4.12
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4J [auth 4]933Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13
EC: 3.6.4.12
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5K [auth 5]775Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM5, CDC46, YLR274W, L9328.1
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6L [auth 6]1,017Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7M [auth 7]845Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase 1-associated factor 1N [auth X]1,238Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: TOF1, YNL273W, N0636
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome segregation in meiosis protein 3O [auth Y]92Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: CSM3, YMR048W, YM9796.01
UniProt
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Entity ID: 6
MoleculeChains LengthOrganismImage
Leading strand DNA template48synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
Lagging strand DNA template20synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
Download Ideal Coordinates CCD File 
CA [auth 7],
P [auth 2],
S [auth 3],
Y [auth 5]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP
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U [auth 4],
X [auth 4]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AA [auth 5],
BA [auth 6],
EA [auth 7],
R [auth 2],
W [auth 4]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
DA [auth 7],
Q [auth 2],
T [auth 3],
V [auth 4],
Z [auth 5]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.0
MODEL REFINEMENTPHENIX1.21-5207

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM152094
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM126907
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA008748

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references