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- PDB-7m10: PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 -

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Basic information

Entry
Database: PDB / ID: 7m10
TitlePHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1
Components
  • Lysine-specific demethylase PHF2
  • Serine/threonine-protein kinase VRK1 N-terminus peptide
KeywordsPROTEIN BINDING / PHD FINGER / METAL-BINDING / ZINC-FINGER / HISTONE-BINDING / NON-HISTONE BINDING
Function / homology
Function and homology information


protein demethylation / histone H4K20 demethylase activity / histone H2AX kinase activity / Golgi disassembly / Cajal body organization / negative regulation of rDNA heterochromatin formation / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor ...protein demethylation / histone H4K20 demethylase activity / histone H2AX kinase activity / Golgi disassembly / Cajal body organization / negative regulation of rDNA heterochromatin formation / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Initiation of Nuclear Envelope (NE) Reformation / Golgi stack / histone H3K4me3 reader activity / nucleosomal DNA binding / histone H3K9 demethylase activity / Cajal body / transcription initiation-coupled chromatin remodeling / transcription coregulator activity / liver development / HDMs demethylate histones / kinetochore / neuron projection development / kinase activity / protein autophosphorylation / histone binding / transcription coactivator activity / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / iron ion binding / cell division / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / nucleolus / signal transduction / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Jumonji, helical domain / Jumonji helical domain / : / : / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger ...Jumonji, helical domain / Jumonji helical domain / : / : / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / 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 / Zinc finger, RING/FYVE/PHD-type / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Lysine-specific demethylase PHF2 / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Biochem.J. / Year: 2021
Title: Histone H3 N-terminal mimicry drives a novel network of methyl-effector interactions.
Authors: Chen, J. / Horton, J. / Sagum, C. / Zhou, J. / Cheng, X. / Bedford, M.T.
History
DepositionMar 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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: Lysine-specific demethylase PHF2
B: Serine/threonine-protein kinase VRK1 N-terminus peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,25610
Polymers9,8492
Non-polymers4078
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.240, 63.717, 103.152
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21A-292-

HOH

31A-307-

HOH

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Components

#1: Protein Lysine-specific demethylase PHF2 / GRC5 / PHD finger protein 2


Mass: 8535.833 Da / Num. of mol.: 1 / Fragment: PHD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF2, CENP-35, KIAA0662 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold plus
References: UniProt: O75151, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Protein/peptide Serine/threonine-protein kinase VRK1 N-terminus peptide / Vaccinia-related kinase 1


Mass: 1313.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q99986, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 3.5M Sodium Formate,100mM TRIS pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→32.5 Å / Num. obs: 33230 / % possible obs: 81.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 9.83 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Net I/σ(I): 20.1
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 991 / CC1/2: 0.74 / CC star: 0.922 / Rpim(I) all: 0.37 / % possible all: 24.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQI

3kqi


Resolution: 1.15→32.5 Å / SU ML: 0.107 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1648 1668 5.02 %
Rwork0.1565 31528 -
obs0.157 33196 81.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.61 Å2
Refinement stepCycle: LAST / Resolution: 1.15→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms615 0 20 124 759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039681
X-RAY DIFFRACTIONf_angle_d0.7847921
X-RAY DIFFRACTIONf_chiral_restr0.081994
X-RAY DIFFRACTIONf_plane_restr0.0059117
X-RAY DIFFRACTIONf_dihedral_angle_d10.8059251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.220.29621670.25971193X-RAY DIFFRACTION40.74
1.26-1.310.2611660.22352378X-RAY DIFFRACTION76.14
1.31-1.370.20951670.16592707X-RAY DIFFRACTION85.54
1.37-1.450.16951670.15422995X-RAY DIFFRACTION94.02
1.45-1.540.1741670.13823127X-RAY DIFFRACTION97.51
1.54-1.660.16771660.13583184X-RAY DIFFRACTION99.11
1.66-1.820.14951670.13573190X-RAY DIFFRACTION98.94
1.82-2.090.14451670.14033174X-RAY DIFFRACTION97.78
2.09-2.630.16151670.15593287X-RAY DIFFRACTION99.65

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