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- PDB-3c9c: Structural Basis of Histone H4 Recognition by p55 -

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Basic information

Entry
Database: PDB / ID: 3c9c
TitleStructural Basis of Histone H4 Recognition by p55
Components
  • Chromatin assembly factor 1 p55 subunit
  • Histone H4, 27-residue peptide
KeywordsTRANSCRIPTION REPRESSOR / p55 / chromatin / epigenetics / WD4 / histone / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / Chromosomal protein / DNA-binding / Nucleosome core / NUCLEAR PROTEIN
Function / homology
Function and homology information


G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / RCAF complex / eggshell chorion gene amplification / Myb complex ...G0 and Early G1 / HDACs deacetylate histones / Regulation of TP53 Activity through Acetylation / Oxidative Stress Induced Senescence / Transcriptional Regulation by E2F6 / Regulation of PTEN gene transcription / Neddylation / RCAF complex / eggshell chorion gene amplification / Myb complex / segment specification / CAF-1 complex / polytene chromosome / facultative heterochromatin formation / nucleosome organization / NURF complex / NuRD complex / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / histone methyltransferase complex / nuclear chromosome / Sin3-type complex / regulation of mitotic cell cycle / heterochromatin formation / nucleosome assembly / structural constituent of chromatin / histone deacetylase binding / nucleosome / chromosome / chromatin organization / histone binding / transcription regulator complex / nucleic acid binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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-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 / Mainly Beta
Similarity search - Domain/homology
: / Histone H4 / Chromatin assembly factor 1 p55 subunit
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSong, J.J. / Garlick, J.D. / Kingston, R.E.
CitationJournal: Genes Dev. / Year: 2008
Title: Structural basis of histone H4 recognition by p55.
Authors: Song, J.J. / Garlick, J.D. / Kingston, R.E.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromatin assembly factor 1 p55 subunit
B: Histone H4, 27-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7969
Polymers52,0102
Non-polymers7877
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.119, 150.119, 97.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chromatin assembly factor 1 p55 subunit / Probable histone-binding protein Caf1 / CAF-1 p55 subunit / dCAF-1 / Nucleosome-remodeling factor ...Probable histone-binding protein Caf1 / CAF-1 p55 subunit / dCAF-1 / Nucleosome-remodeling factor 55 kDa subunit / NURF-55


Mass: 48817.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Caf1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q24572
#2: Protein/peptide Histone H4, 27-residue peptide /


Mass: 3191.853 Da / Num. of mol.: 1 / Fragment: UNP residues 16-42 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is found naturally in Drosophila melanogaster.
References: UniProt: P84040
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd

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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: 6.219 Å3/Da / Density % sol: 80.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 21402 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 28.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.591 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c99

3c99


Resolution: 3.2→50 Å
RfactorNum. reflection% reflection
Rfree0.2422 990 -
Rwork0.2031 --
all-21290 -
obs-20222 95 %
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 7 0 3152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.5

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