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- PDB-5szc: Structure of human Dpf3 double-PHD domain bound to histone H3 tai... -

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Basic information

Entry
Database: PDB / ID: 5szc
TitleStructure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14
Components
  • Histone H3 tail peptide
  • Zinc finger protein DPF3
KeywordsPEPTIDE BINDING PROTEIN / chromatin / modified histone / PHD domain / zinc binding domain / BAF45 / BAF complex / METAL BINDING PROTEIN / PEPTIDE-BINDING PROTEIN
Function / homology
Function and homology information


brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / muscle organ development / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation ...brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / muscle organ development / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / 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 / positive regulation of cell differentiation / 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 / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / 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 / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Zinc finger protein DPF3 / Gene for histone H3 (germline gene)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.193 Å
AuthorsSingh, N. / Local, A. / Shiau, A. / Ren, B. / Corbett, K.D.
CitationJournal: Nat. Genet. / Year: 2018
Title: Identification of H3K4me1-associated proteins at mammalian enhancers.
Authors: Local, A. / Huang, H. / Albuquerque, C.P. / Singh, N. / Lee, A.Y. / Wang, W. / Wang, C. / Hsia, J.E. / Shiau, A.K. / Ge, K. / Corbett, K.D. / Wang, D. / Zhou, H. / Ren, B.
History
DepositionAug 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _struct_keywords.text
Revision 1.2Oct 4, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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: Zinc finger protein DPF3
H: Histone H3 tail peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2657
Polymers14,8852
Non-polymers3805
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-12 kcal/mol
Surface area7380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.321, 39.321, 147.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

21A-643-

HOH

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Components

#1: Protein Zinc finger protein DPF3 / / BRG1-associated factor 45C / BAF45C / Zinc finger protein cer-d4


Mass: 12881.659 Da / Num. of mol.: 1 / Fragment: double-PHD domain (UNP residues 254-368)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92784
#2: Protein/peptide Histone H3 tail peptide


Mass: 2003.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: V9H1G0, UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.92 Å3/Da / Density % sol: 35.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 4% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2016 / Details: Mirror: Rh coated flat, toroidal focusing
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→38.22 Å / Num. obs: 38068 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.5
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.934 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5SZB

5szb


Resolution: 1.193→37.996 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 12.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 5792 8.27 %
Rwork0.1473 --
obs0.1489 70050 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.193→37.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 12 172 1173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091045
X-RAY DIFFRACTIONf_angle_d1.1221420
X-RAY DIFFRACTIONf_dihedral_angle_d13.988390
X-RAY DIFFRACTIONf_chiral_restr0.088153
X-RAY DIFFRACTIONf_plane_restr0.006184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1933-1.20690.24372170.19192042X-RAY DIFFRACTION97
1.2069-1.22110.30541820.27032172X-RAY DIFFRACTION100
1.2211-1.2360.18211820.16732164X-RAY DIFFRACTION100
1.236-1.25160.15872170.13292100X-RAY DIFFRACTION100
1.2516-1.26810.17041830.13662207X-RAY DIFFRACTION100
1.2681-1.28550.1821870.16652101X-RAY DIFFRACTION100
1.2855-1.30380.31742140.24112132X-RAY DIFFRACTION99
1.3038-1.32330.16971960.12762133X-RAY DIFFRACTION100
1.3233-1.3440.15691850.1312123X-RAY DIFFRACTION100
1.344-1.3660.14972010.12832162X-RAY DIFFRACTION100
1.366-1.38960.15972040.11912146X-RAY DIFFRACTION100
1.3896-1.41480.15641870.11852137X-RAY DIFFRACTION100
1.4148-1.4420.14941990.11652167X-RAY DIFFRACTION100
1.442-1.47150.15061940.12522135X-RAY DIFFRACTION100
1.4715-1.50350.13541970.10722174X-RAY DIFFRACTION100
1.5035-1.53840.16471880.10782123X-RAY DIFFRACTION100
1.5384-1.57690.11341940.10562184X-RAY DIFFRACTION99
1.5769-1.61960.15121900.10022097X-RAY DIFFRACTION100
1.6196-1.66720.12971920.10492147X-RAY DIFFRACTION100
1.6672-1.7210.16011890.10152187X-RAY DIFFRACTION100
1.721-1.78250.11081970.11042152X-RAY DIFFRACTION100
1.7825-1.85390.13751910.122144X-RAY DIFFRACTION100
1.8539-1.93830.16881780.17432080X-RAY DIFFRACTION97
1.9383-2.04050.13951870.12692154X-RAY DIFFRACTION100
2.0405-2.16830.15041840.1342164X-RAY DIFFRACTION100
2.1683-2.33570.19961860.18022131X-RAY DIFFRACTION99
2.3357-2.57070.17441960.15442139X-RAY DIFFRACTION100
2.5707-2.94250.17081890.16562159X-RAY DIFFRACTION100
2.9425-3.70680.17431910.16032158X-RAY DIFFRACTION100
3.7068-38.0150.18271950.17222144X-RAY DIFFRACTION100

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