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Yorodumi- EMDB-35660: Composite cryo-EM density map of the dimeric human CAF1-H3-H4 complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35660 | |||||||||||||||||||||||||||||||||
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Title | Composite cryo-EM density map of the dimeric human CAF1-H3-H4 complex | |||||||||||||||||||||||||||||||||
Map data | Composite map | |||||||||||||||||||||||||||||||||
Sample |
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Keywords | Histone chaperone / Chromatin assembly factor / REPLICATION | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / chromo shadow domain binding / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / chromo shadow domain binding / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / positive regulation of stem cell population maintenance / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / 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 / Cyclin E associated events during G1/S transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Packaging Of Telomere Ends / Cyclin A:Cdk2-associated events at S phase entry / 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 / Regulation of TP53 Activity through Acetylation / 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 / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / negative regulation of cell migration / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / negative regulation of transforming growth factor beta receptor signaling pathway / 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 / brain development / 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 / histone deacetylase binding / 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 / Potential therapeutics for SARS / chromosome, telomeric region / cadherin binding / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 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_35660.map.gz | 36.9 MB | EMDB map data format | |
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Header (meta data) | emd-35660-v30.xml emd-35660.xml | 26 KB 26 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35660_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_35660.png | 83.5 KB | ||
Others | emd_35660_half_map_1.map.gz emd_35660_half_map_2.map.gz | 59.3 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35660 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35660 | HTTPS FTP |
-Validation report
Summary document | emd_35660_validation.pdf.gz | 871.3 KB | Display | EMDB validaton report |
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Full document | emd_35660_full_validation.pdf.gz | 870.9 KB | Display | |
Data in XML | emd_35660_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_35660_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35660 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35660 | HTTPS FTP |
-Related structure data
Related structure data | 8iqfMC 7y5kC 7y5lC 7y5oC 7y5uC 7y5vC 7y5wC 7y60C 7y61C 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_35660.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite 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
-Half map: #2
File | emd_35660_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35660_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dimeric CAF1-H3-H4 complex
Entire | Name: Dimeric CAF1-H3-H4 complex |
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Components |
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-Supramolecule #1: Dimeric CAF1-H3-H4 complex
Supramolecule | Name: Dimeric CAF1-H3-H4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 486 KDa |
-Supramolecule #2: CAF-1FL complex
Supramolecule | Name: CAF-1FL complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: H3-H4
Supramolecule | Name: H3-H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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-Macromolecule #1: Chromatin assembly factor 1 subunit A
Macromolecule | Name: Chromatin assembly factor 1 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: Histone-binding protein RBBP4
Macromolecule | Name: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.709527 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN ...String: MADKEAAFDD AVEERVINEE YKIWKKNTPF LYDLVMTHAL EWPSLTAQWL PDVTRPEGKD FSIHRLVLGT HTSDEQNHLV IASVQLPND DAQFDASHYD SEKGEFGGFG SVSGKIEIEI KINHEGEVNR ARYMPQNPCI IATKTPSSDV LVFDYTKHPS K PDPSGECN PDLRLRGHQK EGYGLSWNPN LSGHLLSASD DHTICLWDIS AVPKEGKVVD AKTIFTGHTA VVEDVSWHLL HE SLFGSVA DDQKLMIWDT RSNNTSKPSH SVDAHTAEVN CLSFNPYSEF ILATGSADKT VALWDLRNLK LKLHSFESHK DEI FQVQWS PHNETILASS GTDRRLNVWD LSKIGEEQSP EDAEDGPPEL LFIHGGHTAK ISDFSWNPNE PWVICSVSED NIMQ VWQMA ENIYNDEDPE GSVDPEGQGS UniProtKB: Histone-binding protein RBBP4 |
-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: 2 / 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 |
-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 III |
-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 |