8W7M

Yeast replisome in state V


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

Synergism between CMG helicase and leading strand DNA polymerase at replication fork.

Xu, Z.Feng, J.Yu, D.Huo, Y.Ma, X.Lam, W.H.Liu, Z.Li, X.D.Ishibashi, T.Dang, S.Zhai, Y.

(2023) Nat Commun 14: 5849-5849

  • DOI: https://doi.org/10.1038/s41467-023-41506-0
  • Primary Citation of Related Structures:  
    8KG6, 8KG8, 8KG9, 8W7M, 8W7S

  • PubMed Abstract: 

    The replisome that replicates the eukaryotic genome consists of at least three engines: the Cdc45-MCM-GINS (CMG) helicase that separates duplex DNA at the replication fork and two DNA polymerases, one on each strand, that replicate the unwound DNA. Here, we determined a series of cryo-electron microscopy structures of a yeast replisome comprising CMG, leading-strand polymerase Polε and three accessory factors on a forked DNA. In these structures, Polε engages or disengages with the motor domains of the CMG by occupying two alternative positions, which closely correlate with the rotational movement of the single-stranded DNA around the MCM pore. During this process, the polymerase remains stably coupled to the helicase using Psf1 as a hinge. This synergism is modulated by a concerted rearrangement of ATPase sites to drive DNA translocation. The Polε-MCM coupling is not only required for CMG formation to initiate DNA replication but also facilitates the leading-strand DNA synthesis mediated by Polε. Our study elucidates a mechanism intrinsic to the replisome that coordinates the activities of CMG and Polε to negotiate any roadblocks, DNA damage, and epigenetic marks encountered during translocation along replication forks.


  • Organizational Affiliation

    School of Biological Sciences, The University of Hong Kong, Hong Kong, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2
EC: 3.6.4.12
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4
EC: 3.6.4.12
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5
EC: 3.6.4.12
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7
EC: 3.6.4.12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth A]208Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PSF1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth B]213Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PSF2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth C]194Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PSF3
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth D]294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SLD5
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45K [auth E]650Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC45
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha-binding proteinL [auth F],
M [auth G],
N [auth H]
927Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CTF4
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BP [auth N]689Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DPB2
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (71-mer)O [auth I]71Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
BA [auth 7],
V [auth 4]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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Q [auth 2],
T [auth 3]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth 7],
S [auth 2],
X [auth 4],
Y [auth 5],
Z [auth 6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 7],
R [auth 2],
U [auth 3],
W [auth 4]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARCv3.0.1
RECONSTRUCTIONcryoSPARCv2.15.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16104617
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16103918
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF17112119
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF17101720
The University Grants Committee, Research Grants Council (RGC)Hong KongC7028-19GF
The University Grants Committee, Research Grants Council (RGC)Hong KongC7009-20GF
The University Grants Committee, Research Grants Council (RGC)Hong KongECS26101919
The University Grants Committee, Research Grants Council (RGC)Hong KongGRF16103321

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release