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- PDB-5vtb: Crystal structure of RBBP4 bound to BCL11a peptide -

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Basic information

Entry
Database: PDB / ID: 5vtb
TitleCrystal structure of RBBP4 bound to BCL11a peptide
Components
  • B-cell lymphoma/leukemia 11A
  • Histone-binding protein RBBP4
KeywordsPROTEIN BINDING / RBBP4 / Histone Binding protein / WD40 domain
Function / homology
Function and homology information


negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / CAF-1 complex / regulation of dendrite development / negative regulation of dendrite development / NURF complex ...negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / CAF-1 complex / regulation of dendrite development / negative regulation of dendrite development / NURF complex / negative regulation of axon extension / cellular response to L-glutamate / regulation of cell fate specification / positive regulation of collateral sprouting / negative regulation of stem cell population maintenance / paraspeckles / DNA replication-dependent chromatin assembly / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / ESC/E(Z) complex / ALK mutants bind TKIs / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / SWI/SNF complex / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / ATPase complex / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / protein sumoylation / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / nucleosome binding / 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 / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / positive regulation of neuron projection development / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Signaling by ALK fusions and activated point mutants / nucleosome assembly / negative regulation of neuron projection development / histone binding / postsynapse / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / DNA replication / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / cell cycle / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Zinc finger, C2H2 type / YVTN repeat-like/Quinoprotein amine dehydrogenase / zinc finger / Zinc finger C2H2 type domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Zinc finger, C2H2 type / YVTN repeat-like/Quinoprotein amine dehydrogenase / zinc finger / Zinc finger C2H2 type domain profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone-binding protein RBBP4 / B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Probing the interaction between the histone methyltransferase/deacetylase subunit RBBP4/7 and the transcription factor BCL11A in epigenetic complexes.
Authors: Moody, R.R. / Lo, M.C. / Meagher, J.L. / Lin, C.C. / Stevers, N.O. / Tinsley, S.L. / Jung, I. / Matvekas, A. / Stuckey, J.A. / Sun, D.
History
DepositionMay 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
B: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3923
Polymers50,2992
Non-polymers921
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-0 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.301, 85.264, 87.968
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 / Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / ...Chromatin assembly factor 1 subunit C / CAF-1 subunit C / Chromatin assembly factor I p48 subunit / CAF-I p48 / Nucleosome-remodeling factor subunit RBAP48 / Retinoblastoma-binding protein 4 / RBBP-4 / Retinoblastoma-binding protein p48


Mass: 48457.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: unidentified baculovirus / References: UniProt: Q09028
#2: Protein/peptide B-cell lymphoma/leukemia 11A / BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration ...BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration site 9 protein homolog / EVI-9 / Zinc finger protein 856


Mass: 1842.134 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H165
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG2000 MME, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 15853 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.043 / Rrim(I) all: 0.123 / Χ2: 0.963 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4480.5660.9250.2090.6040.83198.7
2.44-2.498.20.5910.9080.2170.6310.84399.3
2.49-2.538.30.4970.9170.1810.530.86999.3
2.53-2.598.20.4310.9470.1590.460.88599.9
2.59-2.648.40.4030.9430.1480.430.84899.5
2.64-2.78.20.3450.9680.1270.3680.91899.7
2.7-2.778.30.3140.9630.1150.3350.92599.7
2.77-2.858.20.2550.9710.0940.2730.87499.9
2.85-2.938.20.2350.9770.0870.2510.89399.7
2.93-3.028.30.2090.9830.0760.2220.93399.9
3.02-3.138.30.1710.9870.0630.1820.95399.9
3.13-3.268.20.1390.9910.0520.1480.979100
3.26-3.418.30.1110.9940.0420.1191.008100
3.41-3.588.20.0970.9930.0360.1041.104100
3.58-3.818.30.0820.9940.0310.0881.208100
3.81-4.18.30.0690.9970.0250.0741.117100
4.1-4.528.40.0570.9970.0210.0611.11699.9
4.52-5.178.40.050.9970.0190.0541.112100
5.17-6.518.40.0540.9970.020.0580.89599.8
6.51-507.60.0470.9970.0180.0510.91199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4R7A

4r7a


Resolution: 2.4→44.32 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.532 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.244 702 4.71 %RANDOM
Rwork0.201 ---
obs0.203 14917 94 %-
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 36.06 Å2 / Biso min: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.5918 Å20 Å20 Å2
2---2.6279 Å20 Å2
3---0.0361 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.4→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 6 140 2912
Biso mean--46.89 42.41 -
Num. residues----363
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes417HARMONIC5
X-RAY DIFFRACTIONt_it2848HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3194SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2848HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3896HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.45
X-RAY DIFFRACTIONt_other_torsion2.41
LS refinement shellResolution: 2.39→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.264 92 4.25 %
Rwork0.196 2071 -
all0.199 2163 -
obs--75.92 %

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