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- PDB-5vab: Crystal structure of ATXR5 PHD domain in complex with histone H3 -

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Basic information

Entry
Database: PDB / ID: 5vab
TitleCrystal structure of ATXR5 PHD domain in complex with histone H3
Components
  • ATXR5 PHD domain
  • Histone H3 peptide
KeywordsTRANSFERASE/DNA BINDING PROTEIN / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


chromatin => GO:0000785 / 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 => GO:0000785 / 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 / RNA Polymerase I Promoter Escape / transcription coregulator activity / 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 / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
Similarity search - Function
Zinc/RING finger domain, C3HC4 (zinc finger) / SET domain profile. / SET domain / 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/RING finger domain, C3HC4 (zinc finger) / SET domain profile. / SET domain / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Histone H3.1
Similarity search - Component
Biological speciesGlycine max (soybean)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsBergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. ...Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.-F.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Molecular basis for the methylation specificity of ATXR5 for histone H3.
Authors: Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M.S. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.F.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATXR5 PHD domain
F: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6774
Polymers7,5462
Non-polymers1312
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-11 kcal/mol
Surface area4380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.010, 44.010, 71.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21A-236-

HOH

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Components

#1: Protein ATXR5 PHD domain


Mass: 6232.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli) / References: UniProt: I1N521*PLUS
#2: Protein/peptide Histone H3 peptide


Mass: 1313.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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.: 49 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M Hepes (pH 6.5), 10% PEG 6000 and 5% (+/-)-2-methyl-2,4-pentanediol. SET : 50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.13 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 8225 / % possible obs: 99.5 % / Redundancy: 25.59 % / Rsym value: 0.043 / Net I/σ(I): 71.92

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QF3

4qf3


Resolution: 1.702→23.536 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.72
RfactorNum. reflection% reflection
Rfree0.1786 433 5.27 %
Rwork0.1489 --
obs0.1504 8223 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.702→23.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms486 0 2 49 537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005502
X-RAY DIFFRACTIONf_angle_d1.02673
X-RAY DIFFRACTIONf_dihedral_angle_d12.856187
X-RAY DIFFRACTIONf_chiral_restr0.07270
X-RAY DIFFRACTIONf_plane_restr0.00786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7022-1.94840.13731360.09262530X-RAY DIFFRACTION100
1.9484-2.45440.16881400.14692569X-RAY DIFFRACTION100
2.4544-23.53780.19291570.16382691X-RAY DIFFRACTION99

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