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- PDB-3qzv: Crystal Structure of BPTF PHD-linker-bromo in complex with histon... -

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Basic information

Entry
Database: PDB / ID: 3qzv
TitleCrystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide
Components
  • Histone H4
  • Nucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION/NUCLEAR PROTEIN / protein-peptide complex / Zinc finger / alpha helix bundle / 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 / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / cellular response to nerve growth factor stimulus / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / brain development / 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 / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / 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 / Amyloid fiber formation / protein heterodimerization activity / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
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: 1.999 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,5014
Polymers21,3702
Non-polymers1312
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-10 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.525, 38.513, 87.752
Angle α, β, γ (deg.)90.00, 111.20, 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: 20297.057 Da / Num. of mol.: 1 / Fragment: BPTF (UNP Residues 2865-3033)
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: 1073.272 Da / Num. of mol.: 1 / Fragment: Histone H4 7-17 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P62805
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.999→20 Å / Num. obs: 13759 / % possible obs: 98.2 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Χ2: 0.998 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.999-2.057.10.5068780.812196.2
2.05-2.17.40.4428920.829197.2
2.1-2.157.30.3738950.792197.5
2.15-2.227.40.2959200.812197.5
2.22-2.297.50.2488990.886197.8
2.29-2.377.50.1959080.887197.8
2.37-2.477.50.1659070.876198.1
2.47-2.587.40.1399150.921198.1
2.58-2.717.40.1149290.996198.5
2.71-2.887.40.0799080.998198.7
2.88-3.17.40.0659221.16198.7
3.1-3.427.30.0499331.092198.8
3.42-3.917.20.0399341.151199.2
3.91-4.917.10.0339451.315199.3
4.91-207.10.0399741.423199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F6J

2f6j


Resolution: 1.999→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.627 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 1044 7.6 %RANDOM
Rwork0.1823 ---
obs0.1863 13758 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.27 Å2 / Biso mean: 42.786 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20.59 Å2
2--1.95 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.999→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 2 142 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221463
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9821971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8055171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02824.30672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73115252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.741158
X-RAY DIFFRACTIONr_chiral_restr0.080.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211125
X-RAY DIFFRACTIONr_mcbond_it0.5111.5866
X-RAY DIFFRACTIONr_mcangle_it0.98421400
X-RAY DIFFRACTIONr_scbond_it1.6643596
X-RAY DIFFRACTIONr_scangle_it2.784.5571
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 64 -
Rwork0.231 884 -
all-948 -
obs--95.18 %
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)
14.5704-0.9637-4.1715.53955.18047.3913-0.63730.2771-0.2453-0.5060.5083-0.0458-0.1029-0.05880.1290.53580.15270.01240.7776-0.00470.214937.613-15.188-38.77
25.4712-1.7924-1.62242.06650.46293.34340.34060.33040.0738-0.1784-0.2972-0.03010.0370.0351-0.04340.19120.1010.00380.19610.00070.066513.4446.07-15.691
328.11357.7624-0.21311.86451.592210.861-0.74221.3531-0.4771-0.22390.5510.61760.4819-1.66640.19120.2577-0.05380.00780.5349-0.08670.3167-4.0513.683-9.148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 64
2X-RAY DIFFRACTION1A175 - 176
3X-RAY DIFFRACTION2A65 - 174
4X-RAY DIFFRACTION3C7 - 12

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