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- PDB-3cfs: Structural basis of the interaction of RbAp46/RbAp48 with histone H4 -

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Basic information

Entry
Database: PDB / ID: 3cfs
TitleStructural basis of the interaction of RbAp46/RbAp48 with histone H4
Components
  • Histone H4
  • Histone-binding protein RBBP7
KeywordsHISTONE/CHAPERONE / RbAp46/RbAp48 / Chromatin / Histone / WD-40 repeat protein / chaperone / Acetylation / Chromatin regulator / DNA replication / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / Chromosomal protein / Nucleosome core / HISTONE-CHAPERONE COMPLEX
Function / homology
Function and homology information


cellular heat acclimation / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / Sin3-type complex ...cellular heat acclimation / NuRD complex / NURF complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / ESC/E(Z) complex / regulation of stem cell differentiation / response to steroid hormone / ATPase complex / Sin3-type complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Replacement of protamines by nucleosomes in the male pronucleus / 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 / Regulation of TP53 Activity through Acetylation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / negative regulation of cell migration / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / negative regulation of cell growth / brain development / 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 / 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 / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / 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) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / histone binding / Potential therapeutics for SARS / chromosome, telomeric region / DNA replication / chromatin remodeling / Amyloid fiber formation / 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-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
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 / 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-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 / 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-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / Mainly Beta
Similarity search - Domain/homology
ARSENIC / Histone H4 / Histone-binding protein RBBP7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMurzina, N.V. / Pei, X.-Y. / Pratap, J.V. / Sparkes, M. / Vicente-Garcia, J. / Ben-Shahar, T.R. / Verreault, A. / Luisi, B.F. / Laue, E.D.
CitationJournal: Structure / Year: 2008
Title: Structural Basis for the Recognition of Histone H4 by the Histone-Chaperone RbAp46.
Authors: Murzina, N.V. / Pei, X.Y. / Zhang, W. / Sparkes, M. / Vicente-Garcia, J. / Pratap, J.V. / McLaughlin, S.H. / Ben-Shahar, T.R. / Verreault, A. / Luisi, B.F. / Laue, E.D.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Histone-binding protein RBBP7
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7113
Polymers48,6362
Non-polymers751
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4.2 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.665, 85.725, 117.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-binding protein RBBP7 / Retinoblastoma-binding protein 7 / RBBP-7 / Retinoblastoma-binding protein p46 / Histone ...Retinoblastoma-binding protein 7 / RBBP-7 / Retinoblastoma-binding protein p46 / Histone acetyltransferase type B subunit 2 / Nucleosome-remodeling factor subunit RBAP46


Mass: 46937.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP7 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16576
#2: Protein/peptide Histone H4


Mass: 1698.050 Da / Num. of mol.: 1 / Fragment: UNP residues 28 to 42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H4A / Cell line (production host): Tuner(DE3)LacI / Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 18% PEG8000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2006 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→19.5 Å / Num. obs: 18615 / % possible obs: 99.8 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.13 / Rsym value: 0.127 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.409 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD data phased model

Resolution: 2.4→19.53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.405 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24862 935 5.1 %RANDOM
Rwork0.18418 ---
obs0.18745 17375 99.95 %-
all-17375 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.268 Å0.094 Å
Luzzati d res low-6 Å
Luzzati sigma a0.229 Å0.251 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 0 1 210 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0213273
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.751.9264458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46324.845161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71515538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7731514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022515
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.31397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.52143
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.331
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.83622030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.54233223
X-RAY DIFFRACTIONr_scbond_it5.49121421
X-RAY DIFFRACTIONr_scangle_it7.29531235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 69 -
Rwork0.192 1251 -
obs--99.7 %

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