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- PDB-7y5v: Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex -

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Basic information

Entry
Database: PDB / ID: 7y5v
TitleCryo-EM structure of the dimeric human CAF1LC-H3-H4 complex
Components
  • Chromatin assembly factor 1 subunit A
  • Chromatin assembly factor 1 subunit B
  • Histone H3.1Histone H3
  • Histone H4
  • Histone-binding protein RBBP4
KeywordsREPLICATION / Histone chaperone / Chromatin assembly factor
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / chromo shadow domain binding / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / chromo shadow domain binding / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / 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 / Polo-like kinase mediated events / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / 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 / epigenetic regulation of gene expression / Cyclin E associated events during G1/S transition / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Regulation of TP53 Activity through Acetylation / 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 / negative regulation of cell migration / 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 / 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 / brain development / 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 / histone deacetylase binding / 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 / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / cadherin binding / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA repair
Similarity search - Function
Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / 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 / 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 ...Chromatin assembly factor 1 subunit B, C-terminal domain / Chromatin assembly factor 1 subunit Cac2/CHAF1B/FAS2 / Chromatin assembly factor 1 complex p150 subunit, N-terminal / 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 / 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-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsLiu, C.P. / Yu, C. / Yu, Z.Y. / Xu, R.M.
Funding support China, 10items
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 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_entity_assembly / pdbx_database_related / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_entity_assembly.name / _pdbx_database_related.details / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromatin assembly factor 1 subunit A
D: Histone H3.1
E: Histone H4
C: Histone-binding protein RBBP4
B: Chromatin assembly factor 1 subunit B
F: Chromatin assembly factor 1 subunit A
I: Histone H3.1
J: Histone H4
H: Histone-binding protein RBBP4
G: Chromatin assembly factor 1 subunit B


Theoretical massNumber of molelcules
Total (without water)336,97010
Polymers336,97010
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Chromatin assembly factor 1 subunit A / / CAF-1 subunit A


Mass: 47228.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHAF1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13111
#2: Protein Histone H3.1 / Histone H3


Mass: 15437.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#3: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: Protein Histone-binding protein RBBP4 / Retinoblastoma-binding protein 4 / RBBP-4


Mass: 47709.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#5: Protein Chromatin assembly factor 1 subunit B / / CAF-1 subunit B / Chromatin assembly factor I p60 subunit / CAF-I 60 kDa subunit / CAF-I p60 / M- ...CAF-1 subunit B / Chromatin assembly factor I p60 subunit / CAF-I 60 kDa subunit / CAF-I p60 / M-phase phosphoprotein 7


Mass: 46714.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHAF1B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13112

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Dimeric CAF1LC-H3-H4 complexCOMPLEXall0RECOMBINANT
2CAF1LC/RBBP4COMPLEX#1, #4-#51RECOMBINANT
3H3-H4COMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.336 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.5 / Details: 20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24904 / Symmetry type: POINT
Atomic model buildingB value: 321 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 7Y5U

7y5u


Accession code: 7Y5U / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418108
ELECTRON MICROSCOPYf_angle_d0.68224580
ELECTRON MICROSCOPYf_dihedral_angle_d4.7532436
ELECTRON MICROSCOPYf_chiral_restr0.0462728
ELECTRON MICROSCOPYf_plane_restr0.0053184

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