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Yorodumi- EMDB-36013: Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36013 | |||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome | |||||||||||||||||||||||||||||||||
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Sample |
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Keywords | REPLICATION-DNA COMPLEX | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information CAF-1 complex / DNA replication-dependent chromatin assembly / chromo shadow domain binding / 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 / epigenetic regulation of gene expression / Packaging Of Telomere Ends ...CAF-1 complex / DNA replication-dependent chromatin assembly / chromo shadow domain binding / 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 / epigenetic regulation of gene expression / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / cadherin binding / cell cycle / Amyloid fiber formation / protein heterodimerization activity / DNA repair / chromatin binding / chromatin / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||||||||||||||
Authors | Liu CP / Yu ZY / 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_36013.map.gz | 31.8 MB | EMDB map data format | |
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Header (meta data) | emd-36013-v30.xml emd-36013.xml | 26 KB 26 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36013_fsc.xml | 7.7 KB | Display | FSC data file |
Images | emd_36013.png | 98.1 KB | ||
Others | emd_36013_additional_1.map.gz emd_36013_half_map_1.map.gz emd_36013_half_map_2.map.gz | 59.5 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36013 | HTTPS FTP |
-Related structure data
Related structure data | 8j6sMC 7y5kC 7y5lC 7y5oC 7y5uC 7y5vC 7y5wC 7y60C 7y61C 8iqfC 8iqgC 8j6tC M: atomic model generated by this map C: citing same article (ref.) |
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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_36013.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Additional map: sharpened map
File | emd_36013_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36013_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36013_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The CAF-1 bound right-handed Di-tetrasome
Entire | Name: The CAF-1 bound right-handed Di-tetrasome |
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Components |
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-Supramolecule #1: The CAF-1 bound right-handed Di-tetrasome
Supramolecule | Name: The CAF-1 bound right-handed Di-tetrasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #5: Chromatin assembly factor 1 subunit B
Macromolecule | Name: Chromatin assembly factor 1 subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.567348 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKVITCEIAW HNKEPVYSLD FQHGTAGRIH RLASAGVDTN VRIWKVEKGP DGKAIVEFLS NLARHTKAVN VVRFSPTGEI LASGGDDAV ILLWKVNDNK EPEQIAFQDE DEAQLNKENW TVVKTLRGHL EDVYDICWAT DGNLMASASV DNTAIIWDVS K GQKISIFN ...String: MKVITCEIAW HNKEPVYSLD FQHGTAGRIH RLASAGVDTN VRIWKVEKGP DGKAIVEFLS NLARHTKAVN VVRFSPTGEI LASGGDDAV ILLWKVNDNK EPEQIAFQDE DEAQLNKENW TVVKTLRGHL EDVYDICWAT DGNLMASASV DNTAIIWDVS K GQKISIFN EHKSYVQGVT WDPLGQYVAT LSCDRVLRVY SIQKKRVAFN VSKMLSGIGA EGEARSYRMF HDDSMKSFFR RL SFTPDGS LLLTPAGCVE SGENVMNTTY VFSRKNLKRP IAHLPCPGKA TLAVRCCPVY FELRPVVETG VELMSLPYRL VFA VASEDS VLLYDTQQSF PFGYVSNIHY HTLSDISWSS DGAFLAISST DGYCSFVTFE KDELGIPLKE KPVLNMRTPD TAKK TKSQT HRGSSPGPRP VEGTPASRTQ DPSSPGTTPP QARQAPAPTV IRDPPSITPA VKSPLPGPSE EKTLQPSSQN TKAHP SRRV TLNTLQAWSK TTPRRINLTP LKTDTPPSSV PTSVISTPST EEIQSETPGD AQGSPPELKR PRLDENKGGT ESLDP UniProtKB: Chromatin assembly factor 1 subunit B |
-Macromolecule #6: Chromatin assembly factor 1 subunit A
Macromolecule | Name: Chromatin assembly factor 1 subunit A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 107.08032 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MLEELECGAP GARGAATAMD CKDRPAFPVK KLIQARLPFK RLNLVPKGKA DDMSDDQGTS VQSKSPDLEA SLDTLENNCH VGSDIDFRP KLVNGKGPLD NFLRNRIETS IGQSTVIIDL TEDSNEQPDS LVDHNKLNSE ASPSREAING QREDTGDQQG L LKAIQNDK ...String: MLEELECGAP GARGAATAMD CKDRPAFPVK KLIQARLPFK RLNLVPKGKA DDMSDDQGTS VQSKSPDLEA SLDTLENNCH VGSDIDFRP KLVNGKGPLD NFLRNRIETS IGQSTVIIDL TEDSNEQPDS LVDHNKLNSE ASPSREAING QREDTGDQQG L LKAIQNDK LAFPGETLSD IPCKTEEEGV GCGGAGRRGD SQECSPRSCP ELTSGPRMCP RKEQDSWSEA GGILFKGKVP MV VLQDILA VRPPQIKSLP ATPQGKNMTP ESEVLESFPE EDSVLSHSSL SSPSSTSSPE GPPAPPKQHS STSPFPTSTP LRR ITKKFV KGSTEKNKLR LQRDQERLGK QLKLRAEREE KEKLKEEAKR AKEEAKKKKE EEKELKEKER REKREKDEKE KAEK QRLKE ERRKERQEAL EAKLEEKRKK EEEKRLREEE KRIKAEKAEI TRFFQKPKTP QAPKTLAGSC GKFAPFEIKE HMVLA PRRR TAFHPDLCSQ LDQLLQQQSG EFSFLKDLKG RQPLRSGPTH VSTRNADIFN SDVVIVERGK GDGVPERRKF GRMKLL QFC ENHRPAYWGT WNKKTALIRA RDPWAQDTKL LDYEVDSDEE WEEEEPGESL SHSEGDDDDD MGEDEDEDDG FFVPHGY LS EDEGVTEECA DPENHKVRQK LKAKEWDEFL AKGKRFRVLQ PVKIGCVWAA DRDCAGDDLK VLQQFAACFL ETLPAQEE Q TPKASKRERR DEQILAQLLP LLHGNVNGSK VIIREFQEHC RRGLLSNHTG SPRSPSTTYL HTPTPSEDAA IPSKSRLKR LISENSVYEK RPDFRMCWYV HPQVLQSFQQ EHLPVPCQWS YVTSVPSAPK EDSGSVPSTG PSQGTPISLK RKSAGSMCIT QFMKKRRHD GQIGAEDMDG FQADTEEEEE EEGDCMIVDV PDAAEVQAPC GAASGAGGGV GVDTGKATLT ASPLGAS UniProtKB: Chromatin assembly factor 1 subunit A |
-Macromolecule #3: Widom 601 DNA (147-MER)
Macromolecule | Name: Widom 601 DNA (147-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.105727 KDa |
Sequence | String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT) |
-Macromolecule #4: Widom 601 DNA (147-MER)
Macromolecule | Name: Widom 601 DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.64407 KDa |
Sequence | String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG) |
-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 I |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
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-8j6s: |