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

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Basic information

Entry
Database: PDB / ID: 3cfv
TitleStructural basis of the interaction of RbAp46/RbAp48 with histone H4
Components
  • Histone H4 peptide
  • Histone-binding protein RBBP7
KeywordsHISTONE/CHAPERONE / RbAp46/RbAp48 / Chromatin / Histone / WD-40 repeat protein / chaperone / flexib / Chromatin regulator / DNA replication / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat / Chromosomal protein / DNA-binding / 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 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Regulation of TP53 Activity through Acetylation / 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 / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / 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 / negative regulation of cell migration / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / negative regulation of transforming growth factor beta receptor signaling pathway / Transcriptional regulation by small RNAs / 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 / negative regulation of cell growth / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / brain development / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / histone binding / Estrogen-dependent gene expression / 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 / 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 / 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: 2.6 Å
AuthorsPei, X.-Y. / Murzina, N.V. / Zhang, W. / McLaughlin, S. / 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 1.3Apr 3, 2024Group: 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,5756
Polymers98,4254
Non-polymers1502
Water4,954275
1
B: Histone-binding protein RBBP7
E: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2873
Polymers49,2132
Non-polymers751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6.2 kcal/mol
Surface area19350 Å2
MethodPISA
2
A: Histone-binding protein RBBP7
F: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2873
Polymers49,2132
Non-polymers751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8.2 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.661, 44.790, 109.592
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12E
22F

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTYRTYRBA11 - 40814 - 411
21VALVALTYRTYRAC11 - 40814 - 411
12ILEILEGLYGLYEB29 - 416 - 18
22ILEILEGLYGLYFD29 - 416 - 18

NCS ensembles :
ID
1
2

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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: 47172.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP7, RBAP46 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16576
#2: Protein/peptide Histone H4 peptide


Mass: 2040.399 Da / Num. of mol.: 2 / Fragment: UNP residues 25 to 42 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. / References: UniProt: P62805
#3: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2007 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 33119 / % possible obs: 99.9 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 3.3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 18.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.731 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our Rabp46/h4 SAD data phasing model

Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.662 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25675 1577 4.8 %RANDOM
Rwork0.19895 ---
obs0.20178 31416 99.64 %-
all-31416 --
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: 51.119 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å21.39 Å2
2---1.55 Å20 Å2
3---2.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.339 Å
Luzzati d res low-6 Å
Luzzati sigma a0.312 Å0.335 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 2 275 6782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0216711
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8651.9279090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9975809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23524.83323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.201151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4621528
X-RAY DIFFRACTIONr_chiral_restr0.0580.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.32981
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.54423
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5483
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.3105
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.46224068
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.42236591
X-RAY DIFFRACTIONr_scbond_it3.94322612
X-RAY DIFFRACTIONr_scangle_it5.45432499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B3012loose positional0.225
2E105loose positional0.565
1B3012loose thermal1.810
2E105loose thermal1.4410
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 129 -
Rwork0.338 2237 -
obs--98.75 %

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