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- PDB-5xfq: Ternary complex of PHF1, a DNA duplex and a histone peptide -

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Basic information

Entry
Database: PDB / ID: 5xfq
TitleTernary complex of PHF1, a DNA duplex and a histone peptide
Components
  • DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
  • PHD finger protein 1
  • Peptide from Histone H3
KeywordsTRANSCRIPTION/DNA / PHF1 / PCL1 / DNA / histone / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


PRC2 methylates histones and DNA / ESC/E(Z) complex / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...PRC2 methylates histones and DNA / ESC/E(Z) complex / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / 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 / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / centrosome / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / 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 / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Histone H3.1 / Histone H3-7 / PHD finger protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Z. / Li, H.
CitationJournal: Nature / Year: 2017
Title: Polycomb-like proteins link the PRC2 complex to CpG islands
Authors: Li, H. / Liefke, R. / Jiang, J. / Kurland, J.V. / Tian, W. / Deng, P. / Zhang, W. / He, Q. / Patel, D.J. / Bulyk, M.L. / Shi, Y. / Wang, Z.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 1
B: PHD finger protein 1
C: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
D: DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')
E: Peptide from Histone H3
F: Peptide from Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,57214
Polymers86,0496
Non-polymers5238
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-45 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.243, 62.550, 97.338
Angle α, β, γ (deg.)90.00, 103.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PHD finger protein 1 / Protein PHF1 / Polycomb-like protein 1 / mPCl1 / T-complex testis-expressed 3


Mass: 37627.324 Da / Num. of mol.: 2 / Fragment: UNP residues 25-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Phf1, Plc1, Tctex-3, Tctex3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z1B8
#2: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3')


Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Peptide from Histone H3


Mass: 1427.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M Bis-Tris at pH 6.5, 0.05M Ammonium Sulfate, 30% pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32456 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2137 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFN

5xfn


Resolution: 2.4→47.414 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.66
RfactorNum. reflection% reflection
Rfree0.258 1648 5.09 %
Rwork0.2221 --
obs0.224 32405 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5031 506 8 56 5601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055724
X-RAY DIFFRACTIONf_angle_d0.7937832
X-RAY DIFFRACTIONf_dihedral_angle_d18.2462173
X-RAY DIFFRACTIONf_chiral_restr0.03825
X-RAY DIFFRACTIONf_plane_restr0.003913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3949-2.46540.34441330.29842424X-RAY DIFFRACTION95
2.4654-2.54490.30981400.30462525X-RAY DIFFRACTION99
2.5449-2.63590.33351250.29592602X-RAY DIFFRACTION99
2.6359-2.74140.35141450.28272548X-RAY DIFFRACTION99
2.7414-2.86620.36761200.27692592X-RAY DIFFRACTION99
2.8662-3.01720.2991170.2792571X-RAY DIFFRACTION99
3.0172-3.20620.33311400.27072554X-RAY DIFFRACTION99
3.2062-3.45370.30491260.25372590X-RAY DIFFRACTION99
3.4537-3.80120.25051550.22042554X-RAY DIFFRACTION100
3.8012-4.35090.21451400.18732582X-RAY DIFFRACTION99
4.3509-5.48030.21181530.18382593X-RAY DIFFRACTION99
5.4803-47.42360.21441540.17782622X-RAY DIFFRACTION98

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