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Yorodumi- PDB-8xgc: Structure of yeast replisome associated with FACT and histone hex... -
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-Basic information
Entry | Database: PDB / ID: 8xgc | ||||||
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Title | Structure of yeast replisome associated with FACT and histone hexamer, Composite map | ||||||
Components |
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Keywords | REPLICATION / Replisome / FACT / histone hexamer | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Li, N. / Gao, Y. / Yu, D. / Gao, N. / Zhai, Y. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xgc.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8xgc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8xgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xgc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8xgc_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8xgc_validation.xml.gz | 243.6 KB | Display | |
Data in CIF | 8xgc_validation.cif.gz | 379.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/8xgc ftp://data.pdbj.org/pub/pdb/validation_reports/xg/8xgc | HTTPS FTP |
-Related structure data
Related structure data | 38317MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA replication licensing factor ... , 5 types, 5 molecules 23467
#1: Protein | Mass: 98911.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1S9 |
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#2: Protein | Mass: 107653.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24279, DNA helicase |
#3: Protein | Mass: 105138.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30665, DNA helicase |
#5: Protein | Mass: 113110.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53091, DNA helicase |
#6: Protein | Mass: 95049.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4BTB2 |
-Protein , 10 types, 14 molecules 5EFGHIJKNROSPQ
#4: Protein | Mass: 86505.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29496, DNA helicase | ||||||||||||||
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#13: Protein | Mass: 74324.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08032 | ||||||||||||||
#14: Protein | Mass: 104543.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01454 #15: Protein | | Mass: 141296.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53840 #16: Protein | | Mass: 36402.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04659 #17: Protein | | Mass: 124516.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25588 #20: Protein | Mass: 15391.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q536 #21: Protein | Mass: 11395.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02309 #22: Protein | | Mass: 14013.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04911 #23: Protein | | Mass: 14264.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02294 |
-DNA polymerase epsilon ... , 2 types, 2 molecules 89
#7: Protein | Mass: 255992.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P21951, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters |
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#8: Protein | Mass: 78425.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24482 |
-DNA replication complex GINS protein ... , 4 types, 4 molecules ABCD
#9: Protein | Mass: 24230.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12488 |
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#10: Protein | Mass: 29341.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#11: Protein | Mass: 21977.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12146 |
#12: Protein | Mass: 33983.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03406 |
-FACT complex subunit ... , 2 types, 2 molecules LM
#18: Protein | Mass: 118776.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32558 |
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#19: Protein | Mass: 63068.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04636 |
-DNA chain , 2 types, 2 molecules XY
#24: DNA chain | Mass: 15689.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
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#25: DNA chain | Mass: 11935.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Non-polymers , 2 types, 12 molecules
#26: Chemical | ChemComp-ZN / #27: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Endogenous replisomes / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 524000 / Symmetry type: POINT |