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- PDB-3gfc: Crystal Structure of Histone-binding protein RBBP4 -

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Basic information

Entry
Database: PDB / ID: 3gfc
TitleCrystal Structure of Histone-binding protein RBBP4
ComponentsHistone-binding protein RBBP4
KeywordsTRANSCRIPTION / RBBP4 / Histone-binding protein / Structural Genomics / Structural Genomics Consortium / SGC / Cell cycle / Chromatin regulator / DNA replication / Nucleus / Repressor / Transcription regulation / WD repeat
Function / homology
Function and homology information


CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / 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 ...CAF-1 complex / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / 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 / 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 / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...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 / 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-binding protein RBBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAmaya, M.F. / Dong, A. / Li, Z. / He, H. / Ni, S. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Amaya, M.F. / Dong, A. / Li, Z. / He, H. / Ni, S. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Cell / Year: 2011
Title: Structure and function of WD40 domain proteins.
Authors: Xu, C. / Min, J.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-binding protein RBBP4


Theoretical massNumber of molelcules
Total (without water)47,7101
Polymers47,7101
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.645, 87.214, 88.203
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-binding protein RBBP4 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48 / Chromatin assembly ...Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I 48 kDa subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48


Mass: 47709.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 0.2M MgCl2, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→88.04 Å / Num. obs: 17716 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Χ2: 1.088 / Net I/σ(I): 20.495
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.385.90.80617280.7231100
2.38-2.485.90.70317490.7921100
2.48-2.595.90.51217360.811100
2.59-2.7360.36817370.91100
2.73-2.95.90.27117570.9421100
2.9-3.1260.18217521.1161100
3.12-3.4460.11217581.4241100
3.44-3.935.90.07717841.5791100
3.93-4.955.90.05218211.461100
4.95-505.60.04118941.104199

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CFS

3cfs


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.283 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 903 5.1 %RANDOM
Rwork0.214 ---
obs0.217 17716 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.42 Å2 / Biso mean: 28.577 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---2.27 Å20 Å2
3---2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 0 70 2652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212654
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9193634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3395333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22424.425113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43115376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.141158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022028
X-RAY DIFFRACTIONr_nbd_refined0.2230.21095
X-RAY DIFFRACTIONr_nbtor_refined0.30.21722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.22
X-RAY DIFFRACTIONr_mcbond_it0.8271.51727
X-RAY DIFFRACTIONr_mcangle_it1.3822708
X-RAY DIFFRACTIONr_scbond_it2.20731079
X-RAY DIFFRACTIONr_scangle_it3.2724.5926
LS refinement shellResolution: 2.3→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 65 -
Rwork0.275 1165 -
all-1230 -
obs--96.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14650.3083-0.62991.8267-0.28091.15950.0284-0.15580.03290.028-0.0710.01290.0350.13450.04270.0585-0.009-0.00130.1215-0.00640.105716.351920.127213.0848
20.7306-0.072-0.30772.8741-0.10141.24010.0397-0.2785-0.01930.4712-0.0660.44580.09430.06250.02630.156-0.01850.12440.13090.01560.11274.134816.950825.5979
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 286
2X-RAY DIFFRACTION2A287 - 410

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