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Yorodumi- EMDB-38317: Structure of yeast replisome associated with FACT and histone hex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38317 | |||||||||
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Title | Structure of yeast replisome associated with FACT and histone hexamer, Composite map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Replisome / FACT / histone hexamer / REPLICATION | |||||||||
Function / homology | Function and homology information Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / establishment of sister chromatid cohesion / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / FACT complex / Unwinding of DNA / replication fork arrest / regulation of nuclear cell cycle DNA replication ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / establishment of sister chromatid cohesion / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / FACT complex / Unwinding of DNA / replication fork arrest / regulation of nuclear cell cycle DNA replication / Cul8-RING ubiquitin ligase complex / DNA replication initiation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / meiotic chromosome segregation / epsilon DNA polymerase complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / GINS complex / DNA strand elongation involved in mitotic DNA replication / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / regulation of chromatin organization / nuclear DNA replication / mitotic DNA replication preinitiation complex assembly / Assembly of the ORC complex at the origin of replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / HDACs deacetylate histones / mitotic DNA replication / SUMO binding / nucleosome organization / anaphase-promoting complex binding / Activation of the pre-replicative complex / CMG complex / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / single-stranded 3'-5' DNA helicase activity / entrainment of circadian clock / single-stranded DNA 3'-5' DNA exonuclease activity / nuclear pre-replicative complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / Termination of translesion DNA synthesis / replication fork protection complex / mitotic DNA replication checkpoint signaling / mitotic DNA replication initiation / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / double-strand break repair via break-induced replication / SUMOylation of chromatin organization proteins / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / single-stranded DNA helicase activity / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / mitotic sister chromatid cohesion / DNA strand elongation involved in DNA replication / nuclear chromosome / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of transcription by RNA polymerase I / leading strand elongation / replication fork processing / RNA Polymerase I Promoter Escape / DNA unwinding involved in DNA replication / nuclear replication fork / nucleolar large rRNA transcription by RNA polymerase I / mitotic G2 DNA damage checkpoint signaling / 3'-5' DNA helicase activity / DNA replication origin binding / Estrogen-dependent gene expression / rRNA transcription / Dual incision in TC-NER / subtelomeric heterochromatin formation / DNA replication initiation / positive regulation of transcription initiation by RNA polymerase II / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / error-prone translesion synthesis / heterochromatin formation / heterochromatin organization / nucleosome binding / nucleosomal DNA binding / telomere maintenance / nuclear periphery / helicase activity / base-excision repair, gap-filling / meiotic cell cycle / replication fork / transcription elongation by RNA polymerase II / base-excision repair / DNA-templated DNA replication Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Li N / Gao Y / Yu D / Gao N / Zhai Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38317.map.gz | 44.2 MB | EMDB map data format | |
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Header (meta data) | emd-38317-v30.xml emd-38317.xml | 47.1 KB 47.1 KB | Display Display | EMDB header |
Images | emd_38317.png | 117.7 KB | ||
Filedesc metadata | emd-38317.cif.gz | 16.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38317 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38317 | HTTPS FTP |
-Validation report
Summary document | emd_38317_validation.pdf.gz | 419.3 KB | Display | EMDB validaton report |
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Full document | emd_38317_full_validation.pdf.gz | 418.9 KB | Display | |
Data in XML | emd_38317_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | emd_38317_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38317 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38317 | HTTPS FTP |
-Related structure data
Related structure data | 8xgcMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38317.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Endogenous replisomes
+Supramolecule #1: Endogenous replisomes
+Macromolecule #1: DNA replication licensing factor MCM2
+Macromolecule #2: DNA replication licensing factor MCM3
+Macromolecule #3: DNA replication licensing factor MCM4
+Macromolecule #4: Minichromosome maintenance protein 5
+Macromolecule #5: DNA replication licensing factor MCM6
+Macromolecule #6: DNA replication licensing factor MCM7
+Macromolecule #7: DNA polymerase epsilon catalytic subunit A
+Macromolecule #8: DNA polymerase epsilon subunit B
+Macromolecule #9: DNA replication complex GINS protein PSF1
+Macromolecule #10: DNA replication complex GINS protein PSF2
+Macromolecule #11: DNA replication complex GINS protein PSF3
+Macromolecule #12: DNA replication complex GINS protein SLD5
+Macromolecule #13: Cell division control protein 45
+Macromolecule #14: DNA polymerase alpha-binding protein
+Macromolecule #15: Topoisomerase 1-associated factor 1
+Macromolecule #16: Chromosome segregation in meiosis protein 3
+Macromolecule #17: Mediator of replication checkpoint protein 1
+Macromolecule #18: FACT complex subunit SPT16
+Macromolecule #19: FACT complex subunit POB3
+Macromolecule #20: Histone H3
+Macromolecule #21: Histone H4
+Macromolecule #22: Histone H2A.1
+Macromolecule #23: Histone H2B.2
+Macromolecule #24: DNA (51-MER)
+Macromolecule #25: DNA (39-MER)
+Macromolecule #26: ZINC ION
+Macromolecule #27: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 524000 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |