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- PDB-7y5k: Crystal structure of human CAF-1 core complex in spacegroup C2221 -

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Basic information

Entry
Database: PDB / ID: 7y5k
TitleCrystal structure of human CAF-1 core complex in spacegroup C2221
Components
  • Chromatin assembly factor 1 subunit A
  • Chromatin assembly factor 1 subunit B
  • 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 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / unfolded protein binding / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / G-protein, beta subunit / 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-binding protein RBBP4 / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsLiu, C.P. / Wang, M.Z. / Xu, R.M.
Funding support China, 9items
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
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 / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin assembly factor 1 subunit A
C: Histone-binding protein RBBP4
B: Chromatin assembly factor 1 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,8124
Polymers125,7203
Non-polymers921
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-74 kcal/mol
Surface area44370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.870, 169.843, 153.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 31295.924 Da / Num. of mol.: 1
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-binding protein RBBP4 / Retinoblastoma-binding protein 4 / RBBP-4


Mass: 47709.527 Da / Num. of mol.: 1
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
#3: Protein Chromatin assembly factor 1 subunit B / / CAF-1 subunit B


Mass: 46714.941 Da / Num. of mol.: 1
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 7% Tacsimate, pH 6.0, 18% (w/v) PEG 3350, 0.12 M lithium citrate and 0.13 M sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.48→50 Å / Num. obs: 18554 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 70.18 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.1
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.75 / Num. unique obs: 1833

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFC, 3FM0

3gfc

3fm0


Resolution: 3.48→39.33 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1746 10 %
Rwork0.2253 --
obs0.2285 17456 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.48→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7780 0 6 2 7788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017978
X-RAY DIFFRACTIONf_angle_d0.44910827
X-RAY DIFFRACTIONf_dihedral_angle_d4.1051053
X-RAY DIFFRACTIONf_chiral_restr0.0441180
X-RAY DIFFRACTIONf_plane_restr0.0031401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.48-3.590.3268970.2808874X-RAY DIFFRACTION64
3.59-3.70.29621190.28081072X-RAY DIFFRACTION79
3.7-3.830.31121410.28811265X-RAY DIFFRACTION92
3.83-3.990.29581480.27631342X-RAY DIFFRACTION98
3.99-4.170.31741520.24091356X-RAY DIFFRACTION99
4.17-4.390.26121540.2381387X-RAY DIFFRACTION100
4.39-4.660.24661510.20561354X-RAY DIFFRACTION100
4.66-5.020.24261540.19821392X-RAY DIFFRACTION100
5.02-5.530.2411530.2091385X-RAY DIFFRACTION100
5.53-6.320.26291570.22461402X-RAY DIFFRACTION99
6.32-7.950.24831570.2231412X-RAY DIFFRACTION100
7.95-39.330.19011630.17991469X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 51.4486 Å / Origin y: 19.7188 Å / Origin z: -32.8006 Å
111213212223313233
T0.3012 Å2-0.138 Å20.0087 Å2-0.3515 Å2-0.0518 Å2--0.3055 Å2
L1.3362 °2-0.8476 °2-0.2898 °2-1.5144 °20.1286 °2--0.5222 °2
S-0.1069 Å °-0.1641 Å °0.1712 Å °0.2047 Å °0.1486 Å °-0.0267 Å °-0.0526 Å °-0.013 Å °-0.0571 Å °
Refinement TLS groupSelection details: all

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