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- EMDB-35660: Composite cryo-EM density map of the dimeric human CAF1-H3-H4 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35660
TitleComposite cryo-EM density map of the dimeric human CAF1-H3-H4 complex
Map dataComposite map
Sample
  • Complex: Dimeric CAF1-H3-H4 complex
    • Complex: CAF-1FL complex
      • Protein or peptide: Chromatin assembly factor 1 subunit A
      • Protein or peptide: Histone-binding protein RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit B
    • Complex: H3-H4
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
KeywordsHistone chaperone / Chromatin assembly factor / REPLICATION
Function / homology
Function and homology information


CAF-1 complex / chromo shadow domain binding / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation ...CAF-1 complex / chromo shadow domain binding / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / ESC/E(Z) complex / regulation of stem cell differentiation / Polo-like kinase mediated events / Transcription of E2F targets under negative control by DREAM complex / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / Transcriptional Regulation by E2F6 / positive regulation of stem cell population maintenance / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / negative regulation of megakaryocyte differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / protein localization to CENP-A containing chromatin / Cyclin A:Cdk2-associated events at S phase entry / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / Regulation of TP53 Activity through Acetylation / 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 / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / negative regulation of cell migration / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / Regulation of PTEN gene transcription / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / brain development / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / histone deacetylase binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / 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 / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling
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 / 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 complex p150 subunit, acidic region ...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 / 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 complex p150 subunit, acidic region / Chromatin assembly factor 1 subunit A dimerization domain / : / CAF1B/HIR1 beta-propeller domain / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / G-protein, beta subunit / Histone-fold / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 / Histone-binding protein RBBP4 / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLiu CP / 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
DepositionMar 16, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35660.png

Downloads & links

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Map

FileDownload / File: emd_35660.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-16.626684000000001 - 29.294692999999999
Average (Standard dev.)0.0062383255 (±1.2067903)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_35660_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35660_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric CAF1-H3-H4 complex

EntireName: Dimeric CAF1-H3-H4 complex
Components
  • Complex: Dimeric CAF1-H3-H4 complex
    • Complex: CAF-1FL complex
      • Protein or peptide: Chromatin assembly factor 1 subunit A
      • Protein or peptide: Histone-binding protein RBBP4
      • Protein or peptide: Chromatin assembly factor 1 subunit B
    • Complex: H3-H4
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4

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Supramolecule #1: Dimeric CAF1-H3-H4 complex

SupramoleculeName: Dimeric CAF1-H3-H4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 486 KDa

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Supramolecule #2: CAF-1FL complex

SupramoleculeName: CAF-1FL complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4-#5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: H3-H4

SupramoleculeName: H3-H4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Chromatin assembly factor 1 subunit A

MacromoleculeName: Chromatin assembly factor 1 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.08032 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: Histone-binding protein RBBP4

MacromoleculeName: Histone-binding protein RBBP4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.709527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #5: Chromatin assembly factor 1 subunit B

MacromoleculeName: Chromatin assembly factor 1 subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.567348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 VEGTPASRTQ DPSSPGTTPP QARQAPAPTV IRDPPSITPA VKSPLPGPSE EKTLQPSSQN TKAHP SRRV TLNTLQAWSK TTPRRINLTP LKTDTPPSSV PTSVISTPST EEIQSETPGD AQGSPPELKR PRLDENKGGT ESLDP

UniProtKB: Chromatin assembly factor 1 subunit B

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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 III

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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: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101016
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7y5u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 321 / Target criteria: Correlation coefficient
Output model

PDB-8iqf:
Cryo-EM structure of the dimeric human CAF1-H3-H4 complex

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