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

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Basic information

Entry
Database: PDB / ID: 2fsa
TitleCrystal structure of PHD finger-linker-bromodomain fragment of human BPTF in the H3(1-15)K4ME2 bound state
Components
  • Histone H3(1-15)K4me2 peptide
  • bromodomain PHD finger transcription factor
KeywordsTRANSCRIPTION / PHD finger / Bromodomain / peptide complex
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / Chromatin modifying enzymes / telomere organization / methylated histone binding / Interleukin-7 signaling / RNA Polymerase I Promoter Opening ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / Chromatin modifying enzymes / telomere organization / methylated histone binding / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / cellular response to nerve growth factor stimulus / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / brain development / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / cell body / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / cadherin binding / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / dendrite / regulation of DNA-templated transcription / chromatin / 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 / nucleus / metal ion binding / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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
DepositionJan 21, 2006Deposition 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
Revision 1.3Aug 30, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 1.4Nov 15, 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: bromodomain PHD finger transcription factor
B: bromodomain PHD finger transcription factor
C: bromodomain PHD finger transcription factor
P: Histone H3(1-15)K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,58010
Polymers63,1874
Non-polymers3926
Water8,341463
1
A: bromodomain PHD finger transcription factor
P: Histone H3(1-15)K4me2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2554
Polymers22,1242
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: bromodomain PHD finger transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6623
Polymers20,5321
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: bromodomain PHD finger transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6623
Polymers20,5321
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.451, 85.169, 109.567
Angle α, β, γ (deg.)90.00, 99.03, 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: PHD 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): Rosseta2 / References: UniProt: Q7Z7D6, UniProt: Q12830*PLUS
#2: Protein/peptide Histone H3(1-15)K4me2 peptide


Mass: 1592.843 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the peptide was chemically synthesized based on the histone H3 tail (1-15) with K4 dimethylated
References: UniProt: P68431*PLUS
#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


Mass: 18.015 Da / Num. of mol.: 463 / 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: 56.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 4000, 8.5% ISO-PROPANOL, 0.085M HEPES-NA, 15% GLYCEROL ANHYDROUS , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9639 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005 / Details: mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9639 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 54370 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.68 / Num. unique all: 5376 / % possible all: 98.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2F6J

2f6j


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2656 -Random
Rwork0.2 ---
all-52599 --
obs-49943 95.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 6 463 4654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00473
X-RAY DIFFRACTIONc_angle_deg1.03176
X-RAY DIFFRACTIONc_dihedral_angle_d20.68121
X-RAY DIFFRACTIONc_improper_angle_d0.71657
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.255 232 -
Rwork0.2361 --
obs-4753 0.8748 %

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