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- PDB-6aze: Crystal Structure of the BPTF PHD-bromodomain module bound to H3K... -

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Basic information

Entry
Database: PDB / ID: 6aze
TitleCrystal Structure of the BPTF PHD-bromodomain module bound to H3KC4me3 methyl lysine analog
Components
  • ALA-ARG-THR-ML3-GLN-THR
  • Nucleosome-remodeling factor subunit BPTF
KeywordsGENE REGULATION / PHD-finger / bromodomain / histone reader / methyllsine analog / MLA
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / 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 / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / 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 / cell body / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromatin remodeling / cadherin binding / 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 / 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. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 H3.1 / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.451 Å
AuthorsChen, Z. / Ruthenburg, A.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115945 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R21HG007426 United States
American Cancer Society130230- RSG-16-248-01-DMC United States
CitationJournal: To be published
Title: Quantitative and structural assessment of methyllysine analog engagement by cognate binding proteins reveals decrements that can impact qualitative experiment interpretation
Authors: Chen, Z. / Ruthenburg, A.J. / Notti, R.Q. / Ueberheide, B. / Banaszynski, L.A.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
P: ALA-ARG-THR-ML3-GLN-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5964
Polymers20,4652
Non-polymers1312
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, monomeric binding model fits well. No evidence for oligomerization from gel filtration and DLS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-3 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.263, 64.130, 85.670
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 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: 19699.434 Da / Num. of mol.: 1 / Fragment: PHD-bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q12830
#2: Protein/peptide ALA-ARG-THR-ML3-GLN-THR


Mass: 765.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide made by SPSS / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#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.: 102 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1uL complex solution (~8 mg/ml of [1:1.2 protein to peptide molar ratio] in 100 mM KCl, 10 mM HEPES KOH, pH 7.5 and 5 mM DTT) + 1 uL reservoir (12% (w/v) polyethylene glycol 6000, 5% ...Details: 1uL complex solution (~8 mg/ml of [1:1.2 protein to peptide molar ratio] in 100 mM KCl, 10 mM HEPES KOH, pH 7.5 and 5 mM DTT) + 1 uL reservoir (12% (w/v) polyethylene glycol 6000, 5% glycerol, 100 mM KCl, and 10 mM MgCl2 buffer), equilibrated against 1mL of reservoir in Nextal hanging drop plate format.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 6994 / % possible obs: 85.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.103 / Χ2: 1.05 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.45-2.4930.3193071.083176.6
2.49-2.543.10.2733121.002178.4
2.54-2.593.50.2513260.98181.3
2.59-2.643.70.2843321.08185.8
2.64-2.740.2193551.073185.1
2.7-2.764.40.2263551.055186.8
2.76-2.834.60.2093381.097188.3
2.83-2.94.80.1823641.035189.2
2.9-2.994.90.1553641.065189.4
2.99-3.095.20.1533491.051188.6
3.09-3.25.30.1463741.094188.6
3.2-3.325.40.1233421.092188.1
3.32-3.475.40.1133701.063187.7
3.47-3.665.40.093481.082187.4
3.66-3.895.50.0733621.04186.2
3.89-4.185.50.0673501.021185.2
4.18-4.65.40.0653561.06186
4.6-5.265.40.0623570.999184.4
5.26-6.615.30.0773661.024182.6
6.61-2550.0663670.993178.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.66 Å23.62 Å
Translation5.66 Å23.62 Å

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.451→23.623 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.38 / Details: PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 356 5.1 %Random selection
Rwork0.1797 ---
obs0.1814 6975 85.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.51 Å2 / Biso mean: 24.53 Å2 / Biso min: 11.09 Å2
Refinement stepCycle: final / Resolution: 2.451→23.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 2 102 1517
Biso mean--19.18 27.04 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121456
X-RAY DIFFRACTIONf_angle_d1.4691973
X-RAY DIFFRACTIONf_chiral_restr0.056206
X-RAY DIFFRACTIONf_plane_restr0.009252
X-RAY DIFFRACTIONf_dihedral_angle_d15.028542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4507-2.80480.29521130.21532087220083
2.8048-3.53180.22191210.19082270239189
3.5318-23.62460.17741220.15842262238484

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