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- PDB-2f6j: Crystal structure of PHD finger-linker-bromodomain fragment of hu... -

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Basic information

Entry
Database: PDB / ID: 2f6j
TitleCrystal structure of PHD finger-linker-bromodomain fragment of human BPTF in the H3(1-15)K4me3 bound state
Components
  • bromodomain PHD finger transcription factor
  • histone H3, N-terminal
KeywordsTRANSCRIPTION / phd finger / bromo domain / histone tail binding / methylation
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / extracellular exosome / nucleoplasm / 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 / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / 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
Nucleosome-remodeling factor subunit BPTF / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H. / Patel, D.J.
CitationJournal: Nature / Year: 2006
Title: Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
Authors: Li, H. / Ilin, S. / Wang, W. / Duncan, E.M. / Wysocka, J. / Allis, C.D. / Patel, D.J.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bromodomain PHD finger transcription factor
B: bromodomain PHD finger transcription factor
C: bromodomain PHD finger transcription factor
P: histone H3, N-terminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,59510
Polymers63,2024
Non-polymers3926
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.579, 84.987, 109.385
Angle α, β, γ (deg.)90.00, 99.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein bromodomain PHD finger transcription factor


Mass: 20531.531 Da / Num. of mol.: 3 / Fragment: finger-linker-bromodomain (residues 2583-2751)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF / Plasmid: pGex6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q7Z7D6, UniProt: Q12830*PLUS
#2: Protein/peptide histone H3, N-terminal /


Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: residues 4-18 / Source method: obtained synthetically
Details: This sequence is modified from human histone HIST1H3I, GenBankAAH69305 residues 4-18
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4000, 8.5% iso-Propanol, 0.085M Hepes-Na pH 7.5, 15% Glycerol anhydrous, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.3477 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3477 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 47113 / Num. obs: 46877 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3733 8.1 %Random
Rwork0.198 ---
all-47113 --
obs-45999 97.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.071 Å20 Å2-2.814 Å2
2--1.211 Å20 Å2
3----3.282 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.25 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 6 451 4643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.728
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.249 350
Rwork0.22 -
obs-4313

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