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- EMDB-33630: Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome -

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Entry
Database: EMDB / ID: EMD-33630
TitleCryo-EM structure of human CAF1LC bound right-handed Di-tetrasome
Map datamap
Sample
  • Complex: The CAF1LC bound right-handed Di-tetrasome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • DNA: Widom 601 DNA (147-MER)
    • DNA: Widom 601 DNA (147-MER)
    • Protein or peptide: Chromatin assembly factor 1 subunit A
    • Protein or peptide: Chromatin assembly factor 1 subunit B
KeywordsREPLICATION
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 / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / histone binding / gene expression / 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
Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor complex 1 subunit p60, C-terminal / : / Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A ...Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor complex 1 subunit p60, C-terminal / : / Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / G-protein, beta subunit / Histone-fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3.1 / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLiu CP / Yu C / Yu ZY / Xu RM
Funding support China, 10 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31991162 China
National Natural Science Foundation of China (NSFC)91853204 China
National Natural Science Foundation of China (NSFC)92153302 China
National Natural Science Foundation of China (NSFC)31300614 China
Ministry of Science and Technology (MoST, China)2019YFA0508900 China
Ministry of Science and Technology (MoST, China)2018YFE0203300 China
Ministry of Science and Technology (MoST, China)2017YFA0506600 China
Chinese Academy of SciencesXDB37010100 China
Chinese Academy of Sciences2018125 China
Chinese Academy of Sciences2017131 China
CitationJournal: 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
DepositionJun 18, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33630.png

Downloads & links

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Map

FileDownload / File: emd_33630.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.13548346 - 0.45660624
Average (Standard dev.)0.00039379415 (±0.0173036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33630_msk_1.map
Projections & Slices
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Additional map: sharped map

Fileemd_33630_additional_1.map
Annotationsharped map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map

Fileemd_33630_half_map_1.map
Annotationhalf_B map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half A map

Fileemd_33630_half_map_2.map
Annotationhalf_A map
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Sample components

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Entire : The CAF1LC bound right-handed Di-tetrasome

EntireName: The CAF1LC bound right-handed Di-tetrasome
Components
  • Complex: The CAF1LC bound right-handed Di-tetrasome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • DNA: Widom 601 DNA (147-MER)
    • DNA: Widom 601 DNA (147-MER)
    • Protein or peptide: Chromatin assembly factor 1 subunit A
    • Protein or peptide: Chromatin assembly factor 1 subunit B

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Supramolecule #1: The CAF1LC bound right-handed Di-tetrasome

SupramoleculeName: The CAF1LC bound right-handed Di-tetrasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #5: Chromatin assembly factor 1 subunit A

MacromoleculeName: Chromatin assembly factor 1 subunit A / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.228848 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KAEITRFFQK PKTPQAPKTL AGSCGKFAPF EIKEHMVLAP RRRTAFHPDL CSQLDQLLQQ QSGEFSFLKD LKGRQPLRSG PTHVSTRNA DIFNSDVVIV ERGKGDGVPE RRKFGRMKLL QFCENHRPAY WGTWNKKTAL IRARDPWAQD TKLLDYEVDS D EEWEEEEP ...String:
KAEITRFFQK PKTPQAPKTL AGSCGKFAPF EIKEHMVLAP RRRTAFHPDL CSQLDQLLQQ QSGEFSFLKD LKGRQPLRSG PTHVSTRNA DIFNSDVVIV ERGKGDGVPE RRKFGRMKLL QFCENHRPAY WGTWNKKTAL IRARDPWAQD TKLLDYEVDS D EEWEEEEP GESLSHSEGD DDDDMGEDED EDDGFFVPHG YLSEDEGVTE ECADPENHKV RQKLKAKEWD EFLAKGKRFR VL QPVKIGC VWAADRDCAG DDLKVLQQFA ACFLETLPAQ EEQTPKASKR ERRDEQILAQ LLPLLHGNVN GSKVIIREFQ EHC RRGLLS NHTGSPRSPS TTYLHTPTPS EDAAIPSKSR LKRLISENSV YEKRPDFRMC WYVHPQVLQS FQQEHLPVPC QWSY VTSVP SAPKEDS

UniProtKB: Chromatin assembly factor 1 subunit A

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Macromolecule #6: Chromatin assembly factor 1 subunit B

MacromoleculeName: Chromatin assembly factor 1 subunit B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.714941 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 VEGT

UniProtKB: Chromatin assembly factor 1 subunit B

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Macromolecule #3: Widom 601 DNA (147-MER)

MacromoleculeName: Widom 601 DNA (147-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.105727 KDa
SequenceString: (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)

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Macromolecule #4: Widom 601 DNA (147-MER)

MacromoleculeName: Widom 601 DNA (147-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.64407 KDa
SequenceString: (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)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5 / Details: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178734
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-7y60:
Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome

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