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- PDB-3qzt: Crystal Structure of BPTF bromo in complex with histone H4K16ac -... -

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Basic information

Entry
Database: PDB / ID: 3qzt
TitleCrystal Structure of BPTF bromo in complex with histone H4K16ac - Form II
Components
  • Histone H4
  • Nucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION/NUCLEAR PROTEIN / protein-peptide complex / all alpha helix / transcription / histone h4 / nuclear / TRANSCRIPTION-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / 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 / methylated histone binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / cellular response to nerve growth factor stimulus / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / brain development / 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 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell body / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromosome, telomeric region / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / dendrite / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / 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 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLi, H. / Ruthenburg, A.J. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions.
Authors: Ruthenburg, A.J. / Li, H. / Milne, T.A. / Dewell, S. / McGinty, R.K. / Yuen, M. / Ueberheide, B. / Dou, Y. / Muir, T.W. / Patel, D.J. / Allis, C.D.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7193
Polymers14,6272
Non-polymers921
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.693, 27.163, 58.444
Angle α, β, γ (deg.)90.00, 115.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF / Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal ...Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal Alzheimer antigen


Mass: 13443.338 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 2924-3037)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2 / References: UniProt: Q12830
#2: Protein/peptide Histone H4 /


Mass: 1183.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P62805
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 19449 / % possible obs: 98.1 % / Rmerge(I) obs: 0.073 / Χ2: 1.271 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.550.48719071.121197.7
1.55-1.620.41418701.111196.3
1.62-1.690.33419361.146197.4
1.69-1.780.2619211.191198.9
1.78-1.890.18819321.222198.1
1.89-2.040.12219551.353198.4
2.04-2.240.08419581.581198.8
2.24-2.560.06619641.439198.8
2.56-3.230.05219921.441199.5
3.23-200.0420141.032197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F6J

2f6j


Resolution: 1.5→19.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1984 / WRfactor Rwork: 0.1638 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8994 / SU B: 2.415 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0746 / SU Rfree: 0.0779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 1529 7.9 %RANDOM
Rwork0.1638 ---
obs0.1664 19406 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 265.65 Å2 / Biso mean: 18.07 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å21.07 Å2
2---0.4 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 6 139 1102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221036
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.991406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41822.96354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4161510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021806
X-RAY DIFFRACTIONr_mcbond_it1.2191.5596
X-RAY DIFFRACTIONr_mcangle_it2.1662973
X-RAY DIFFRACTIONr_scbond_it3.3153440
X-RAY DIFFRACTIONr_scangle_it5.3774.5425
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 117 -
Rwork0.257 1232 -
all-1349 -
obs--94.53 %
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)
10.3229-0.0396-0.09270.3397-0.03950.4040.0002-0.0086-0.00740.01450.00090.01530.0078-0.0135-0.00110.0009-0.00040.00060.00090.00020.000813.5127-0.276214.011
22.46751.7041-0.34113.4134-0.90421.0446-0.00810.143-0.0861-0.0155-0.1429-0.35390.13960.07970.1510.02320.00610.00840.04110.01630.071231.84223.027113.6617
311.12113.5422.172916.49072.64650.4250.0351-0.02380.23960.075-0.05040.28610.0122-0.0010.01540.01940.02780.01510.10490.00280.097525.3753-7.6257-0.6838
40.1784-0.0097-0.05530.3355-0.04450.25490.0048-0.0045-0.00640.0142-0.0055-0.00980.0129-0.01530.00070.0265-0.0029-0.00040.0272-0.00370.022515.3567-0.91713.5604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A66 - 173
2X-RAY DIFFRACTION2B14 - 19
3X-RAY DIFFRACTION3A1
4X-RAY DIFFRACTION4A2 - 59
5X-RAY DIFFRACTION4A175 - 250

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