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- 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 | ||||||
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![]() | REPLICATION / Replisome / FACT / histone hexamer | ||||||
Function / homology | ![]() 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 / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / epsilon DNA polymerase complex / 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 / anaphase-promoting complex binding / Activation of the pre-replicative complex / CMG complex / nucleosome organization / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / nuclear pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / 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 / mitotic DNA replication checkpoint signaling / replication fork protection complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / cellular response to osmotic stress / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / single-stranded DNA helicase activity / 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 / nucleotide-excision repair, DNA gap filling / mitotic sister chromatid cohesion / DNA replication proofreading / 3'-5' DNA helicase activity / 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 / DNA unwinding involved in DNA replication / replication fork processing / leading strand elongation / RNA Polymerase I Promoter Escape / nuclear replication fork / nucleolar large rRNA transcription by RNA polymerase I / mitotic G2 DNA damage checkpoint signaling / DNA replication origin binding / Estrogen-dependent gene expression / rRNA transcription / Dual incision in TC-NER / DNA replication initiation / subtelomeric heterochromatin formation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / Ub-specific processing proteases / error-prone translesion synthesis / nucleosomal DNA binding / DNA helicase activity / telomere maintenance / nuclear periphery / base-excision repair, gap-filling / meiotic cell cycle / replication fork / helicase activity / transcription elongation by RNA polymerase II / base-excision repair / heterochromatin formation / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / structural constituent of chromatin Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | Li, N. / Gao, Y. / Yu, D. / Gao, N. / Zhai, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 38317MC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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) ![]() ![]() |
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#2: Protein | Mass: 107653.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 105138.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 113110.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 95049.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() | ||||||||||||||
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#13: Protein | Mass: 74324.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||
#14: Protein | Mass: 104543.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 141296.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | | Mass: 36402.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | | Mass: 124516.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #20: Protein | Mass: 15391.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #21: Protein | Mass: 11395.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: Protein | | Mass: 14013.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: Protein | | Mass: 14264.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() 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) ![]() ![]() |
-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) ![]() ![]() |
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#10: Protein | Mass: 29341.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 21977.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 33983.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#19: Protein | Mass: 63068.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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) ![]() ![]() |
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#25: DNA chain | Mass: 11935.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 2 types, 12 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#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 |
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Sample preparation
Component | Name: Endogenous replisomes / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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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 |