8XGC

Structure of yeast replisome associated with FACT and histone hexamer, Composite map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Parental histone transfer caught at the replication fork.

Li, N.Gao, Y.Zhang, Y.Yu, D.Lin, J.Feng, J.Li, J.Xu, Z.Zhang, Y.Dang, S.Zhou, K.Liu, Y.Li, X.D.Tye, B.K.Li, Q.Gao, N.Zhai, Y.

(2024) Nature 627: 890-897

  • DOI: https://doi.org/10.1038/s41586-024-07152-2
  • Primary Citation of Related Structures:  
    8XGC

  • PubMed Abstract: 

    In eukaryotes, DNA compacts into chromatin through nucleosomes 1,2 . Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin 3,4 . Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A-H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3-H4 tetramer, while the vacant H2A-H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3-H4 dimer and extends across the tetramerization interface of the H3-H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3-H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
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 
EC: 3.6.4.12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AG [auth 8]2,222Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BH [auth 9]689Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1I [auth A]208Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2J [auth B]251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3K [auth C]194Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5L [auth D]294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45M [auth E]650Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha-binding proteinN [auth F],
O [auth G],
P [auth H]
927Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Topoisomerase 1-associated factor 1Q [auth I]1,238Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome segregation in meiosis protein 3R [auth J]317Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of replication checkpoint protein 1S [auth K]1,096Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit SPT16T [auth L]1,035Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit POB3U [auth M]552Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3V [auth N],
Z [auth R]
136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4AA [auth S],
W [auth O]
103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.1X [auth P]132Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.2Y [auth Q]131Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains LengthOrganismImage
DNA (51-MER)BA [auth X]51Saccharomyces cerevisiae
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Entity ID: 25
MoleculeChains LengthOrganismImage
DNA (39-MER)CA [auth Y]39Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

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EA [auth 2],
FA [auth 3],
IA [auth 5],
KA [auth 6],
MA [auth 7]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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DA [auth 2]
GA [auth 4]
HA [auth 5]
JA [auth 6]
LA [auth 7]
DA [auth 2],
GA [auth 4],
HA [auth 5],
JA [auth 6],
LA [auth 7],
NA [auth 8],
OA [auth 8]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references
  • Version 1.2: 2024-04-10
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary