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- PDB-7y5o: Crystal structure of human CAF-1 core complex in spacegroup P21 -

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Basic information

Entry
Database: PDB / ID: 7y5o
TitleCrystal structure of human CAF-1 core complex in spacegroup P21
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 / 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 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of cell migration / Regulation of PTEN gene transcription / 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) / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / unfolded protein binding / nucleosome assembly / histone binding / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 / : / G-protein, beta subunit / 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-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: 3.57 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen
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
B: Chromatin assembly factor 1 subunit B
C: Histone-binding protein RBBP4
D: Chromatin assembly factor 1 subunit A
E: Chromatin assembly factor 1 subunit B
F: Histone-binding protein RBBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,90111
Polymers251,4416
Non-polymers4605
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.613, 176.092, 100.913
Angle α, β, γ (deg.)90.00, 115.09, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_1ens_2
d_2ens_2
d_1ens_3
d_2ens_3

NCS ensembles :
ID
ens_2
ens_1
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.427484680971, 0.00855616711953, -0.903982101338), (0.00045170553369, -0.999957106924, -0.00925096073347), (-0.904022479531, 0.00354631028029, -0.427470209706)12.1159483512, -0.457687104456, 18.9926233398
2given(0.430681524607, -0.00106179024117, -0.902503350112), (-0.00202256629513, -0.999997932285, 0.000211307924857), (-0.902501708357, 0.00173436643794, -0.430682781621)11.8427197758, -0.328664266448, 18.8310939271
3given(0.430142429646, 0.0100085963357, -0.902705554551), (-0.00758418810753, -0.999863189978, -0.0146997081074), (-0.902729178829, 0.0131692568918, -0.430007674773)12.264788257, -0.666058946612, 19.3652642417

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Components

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


Mass: 31295.924 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 Chromatin assembly factor 1 subunit B / CAF-1 subunit B


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
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.22 Å3/Da / Density % sol: 66.31 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
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: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.57→50 Å / Num. obs: 56505 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 50.77 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 0.584 / Num. unique obs: 2062

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y5K

7y5k


Resolution: 3.57→26.98 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 3289 5.82 %
Rwork0.2142 --
obs0.2153 56505 75.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.57→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15514 0 30 17 15561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215927
X-RAY DIFFRACTIONf_angle_d0.46421611
X-RAY DIFFRACTIONf_dihedral_angle_d4.2092102
X-RAY DIFFRACTIONf_chiral_restr0.0442356
X-RAY DIFFRACTIONf_plane_restr0.0032790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.57-3.620.2818620.2813804X-RAY DIFFRACTION27
3.62-3.680.2363740.28231073X-RAY DIFFRACTION36
3.68-3.740.3572660.27591270X-RAY DIFFRACTION40
3.74-3.80.2238860.26551304X-RAY DIFFRACTION45
3.8-3.870.2753970.27381544X-RAY DIFFRACTION49
3.87-3.950.2912930.26121615X-RAY DIFFRACTION54
3.95-4.030.28761240.25781842X-RAY DIFFRACTION60
4.03-4.110.26681250.24591965X-RAY DIFFRACTION66
4.11-4.210.25621360.24392158X-RAY DIFFRACTION70
4.21-4.310.28151550.23782260X-RAY DIFFRACTION74
4.31-4.430.24761450.22282431X-RAY DIFFRACTION81
4.43-4.560.22281310.20352556X-RAY DIFFRACTION82
4.56-4.710.17841600.20622609X-RAY DIFFRACTION86
4.71-4.870.20141300.19212760X-RAY DIFFRACTION91
4.87-5.070.2211580.19452921X-RAY DIFFRACTION94
5.07-5.30.2331940.20422962X-RAY DIFFRACTION97
5.3-5.570.23881900.21793008X-RAY DIFFRACTION99
5.57-5.920.26461770.23273060X-RAY DIFFRACTION100
5.92-6.370.26812040.22483008X-RAY DIFFRACTION100
6.37-70.23741960.22413028X-RAY DIFFRACTION100
7-7.990.24511960.20123010X-RAY DIFFRACTION100
7.99-9.980.18741950.17243038X-RAY DIFFRACTION99
9.99-26.980.15421950.15562990X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 9.8915 Å / Origin y: -0.2377 Å / Origin z: 7.0164 Å
111213212223313233
T0.3551 Å2-0.0077 Å20.0114 Å2-0.2827 Å2-0.0283 Å2--0.3283 Å2
L0.6644 °20.1498 °2-0.0219 °2-0.2968 °20.1311 °2--0.4721 °2
S0.0641 Å °-0.0772 Å °0.0484 Å °0.0271 Å °-0.0259 Å °-0.03 Å °-0.0309 Å °-0.0621 Å °-0.0274 Å °
Refinement TLS groupSelection details: all

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