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Yorodumi- EMDB-33631: Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33631 | |||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome | |||||||||||||||||||||||||||||||||
Map data | map | |||||||||||||||||||||||||||||||||
Sample |
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Keywords | 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 / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / unfolded protein binding / nucleosome / 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 / gene expression / Processing of DNA double-strand break ends / 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 | single particle reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||||||||||||||||||||||||||
Authors | Liu CP / Yu ZY / Yu C / Xu RM | |||||||||||||||||||||||||||||||||
Funding support | China, 10 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33631.map.gz | 30.8 MB | EMDB map data format | |
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Header (meta data) | emd-33631-v30.xml emd-33631.xml | 28.2 KB 28.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33631_fsc.xml | 7.7 KB | Display | FSC data file |
Images | emd_33631.png | 68.8 KB | ||
Masks | emd_33631_msk_1.map | 64 MB | Mask map | |
Others | emd_33631_additional_1.map.gz emd_33631_half_map_1.map.gz emd_33631_half_map_2.map.gz | 59.7 MB 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33631 | HTTPS FTP |
-Validation report
Summary document | emd_33631_validation.pdf.gz | 737 KB | Display | EMDB validaton report |
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Full document | emd_33631_full_validation.pdf.gz | 736.6 KB | Display | |
Data in XML | emd_33631_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | emd_33631_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33631 | HTTPS FTP |
-Related structure data
Related structure data | 7y61MC 7y5kC 7y5lC 7y5oC 7y5uC 7y5vC 7y5wC 7y60C 8iqfC 8iqgC 8j6sC 8j6tC 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_33631.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33631_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharped map
File | emd_33631_additional_1.map | ||||||||||||
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Annotation | sharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half A map
File | emd_33631_half_map_1.map | ||||||||||||
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Annotation | half_A map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half B map
File | emd_33631_half_map_2.map | ||||||||||||
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Annotation | half_B map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Two CAF1LCs bound right-handed Di-tetrasome
+Supramolecule #1: Two CAF1LCs bound right-handed Di-tetrasome
+Supramolecule #2: Histone H4/H3.1
+Supramolecule #3: DNA
+Supramolecule #4: Chromatin assembly factor 1 subunit A/B
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #5: Chromatin assembly factor 1 subunit A
+Macromolecule #6: Chromatin assembly factor 1 subunit B
+Macromolecule #3: Widom 601 DNA (147-MER)
+Macromolecule #4: Widom 601 DNA (147-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |
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Output model | PDB-7y61: |