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- EMDB-38316: Structure of yeast replisome associated with FACT and histone hex... -

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Entry
Database: EMDB / ID: EMD-38316
TitleStructure of yeast replisome associated with FACT and histone hexamer, Conformation-1
Map data
Sample
  • Complex: Endogenous replisomes
KeywordsReplisome / FACT / histone hexamer / REPLICATION
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi N / Gao Y / Yu D / Gao N / Zhai Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Parental histone transfer caught at the replication fork.
Authors: Ningning Li / Yuan Gao / Yujie Zhang / Daqi Yu / Jianwei Lin / Jianxun Feng / Jian Li / Zhichun Xu / Yingyi Zhang / Shangyu Dang / Keda Zhou / Yang Liu / Xiang David Li / Bik Kwoon Tye / ...Authors: Ningning Li / Yuan Gao / Yujie Zhang / Daqi Yu / Jianwei Lin / Jianxun Feng / Jian Li / Zhichun Xu / Yingyi Zhang / Shangyu Dang / Keda Zhou / Yang Liu / Xiang David Li / Bik Kwoon Tye / Qing Li / Ning Gao / Yuanliang Zhai /
Abstract: In eukaryotes, DNA compacts into chromatin through nucleosomes. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin. Here we report cryo- ...In eukaryotes, DNA compacts into chromatin through nucleosomes. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin. 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.
History
DepositionDec 15, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38316.png

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Map

FileDownload / File: emd_38316.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.8219435 - 4.9707947
Average (Standard dev.)0.0061271423 (±0.22072159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38316_half_map_1.map
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Half map: #2

Fileemd_38316_half_map_2.map
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Sample components

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Entire : Endogenous replisomes

EntireName: Endogenous replisomes
Components
  • Complex: Endogenous replisomes

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Supramolecule #1: Endogenous replisomes

SupramoleculeName: Endogenous replisomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72000

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