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Yorodumi- PDB-8j6t: Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j6t | |||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome | |||||||||||||||||||||||||||||||||
Components |
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Keywords | REPLICATION/DNA / REPLICATION-DNA COMPLEX | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information CAF-1 complex / chromo shadow domain binding / DNA replication-dependent chromatin assembly / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine ...CAF-1 complex / chromo shadow domain binding / DNA replication-dependent chromatin assembly / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / unfolded protein binding / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / DNA repair / chromatin binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||||||||||||||||||||||||||
Authors | Liu, C.P. / Yu, Z.Y. / Xu, R.M. | |||||||||||||||||||||||||||||||||
Funding support | China, 10items
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Citation | Journal: Science / Year: 2023 Title: Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. Authors: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng ...Authors: Chao-Pei Liu / Zhenyu Yu / Jun Xiong / Jie Hu / Aoqun Song / Dongbo Ding / Cong Yu / Na Yang / Mingzhu Wang / Juan Yu / Peini Hou / Kangning Zeng / Zhenyu Li / Zhuqiang Zhang / Xinzheng Zhang / Wei Li / Zhiguo Zhang / Bing Zhu / Guohong Li / Rui-Ming Xu / Abstract: Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly ...Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j6t.cif.gz | 337.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j6t.ent.gz | 203.5 KB | Display | PDB format |
PDBx/mmJSON format | 8j6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j6t_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8j6t_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8j6t_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 8j6t_validation.cif.gz | 72.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/8j6t ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j6t | HTTPS FTP |
-Related structure data
Related structure data | 36014MC 7y5kC 7y5lC 7y5oC 7y5uC 7y5vC 7y5wC 7y60C 7y61C 8iqfC 8iqgC 8j6sC M: map data used to model this data C: citing same article (ref.) |
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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
-Protein , 2 types, 8 molecules GECAHFDB
#1: Protein | Mass: 15437.167 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805 |
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-Widom 601 DNA (147- ... , 2 types, 2 molecules IJ
#3: DNA chain | Mass: 45105.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 45644.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Chromatin assembly factor 1 subunit ... , 2 types, 4 molecules KMLN
#5: Protein | Mass: 107080.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHAF1A / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q13111 #6: Protein | Mass: 61567.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHAF1B / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q13112 |
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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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 / Details: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13993 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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