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- PDB-3kqi: crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide -

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Basic information

Entry
Database: PDB / ID: 3kqi
Titlecrystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide
Components
  • H3K4Me3 peptide
  • PHD finger protein 2
KeywordsNUCLEAR PROTEIN / PHD finger / Metal-binding / Zinc-finger / Histone-binding
Function / homology
Function and homology information


protein demethylation / histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / 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 / histone H3K4me3 reader activity / histone H3K9 demethylase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening ...protein demethylation / histone H4K20 demethylase activity / negative regulation of rDNA heterochromatin formation / 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 / histone H3K4me3 reader activity / histone H3K9 demethylase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / transcription initiation-coupled chromatin remodeling / 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 / epigenetic regulation of gene expression / 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 / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription coregulator activity / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / liver development / 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 / kinetochore / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / 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 / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / transcription coactivator activity / chromatin remodeling / cadherin binding / Amyloid fiber formation / iron ion binding / protein heterodimerization activity / regulation of transcription by RNA polymerase II / nucleolus / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Jumonji, helical domain / Jumonji helical domain / : / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / JmjC domain, hydroxylase / Herpes Virus-1 / Zinc finger, PHD-type, conserved site ...Jumonji, helical domain / Jumonji helical domain / : / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / JmjC domain, hydroxylase / 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 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase PHF2 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsWen, H. / Li, J.Z. / Song, T. / Lu, M. / Lee, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.
Authors: Wen, H. / Li, J. / Song, T. / Lu, M. / Kan, P.Y. / Lee, M.G. / Sha, B. / Shi, X.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 13, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 2
B: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2338
Polymers9,9262
Non-polymers3076
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-30 kcal/mol
Surface area5810 Å2
MethodPISA
2
A: PHD finger protein 2
B: H3K4Me3 peptide
hetero molecules

A: PHD finger protein 2
B: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,46716
Polymers19,8534
Non-polymers61412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4390 Å2
ΔGint-76 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.757, 77.758, 72.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein PHD finger protein 2 / GRC5


Mass: 8575.896 Da / Num. of mol.: 1 / Fragment: PHD finger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0662, PHF2 / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75151
#2: Protein/peptide H3K4Me3 peptide


Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P68431

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Non-polymers , 5 types, 131 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 11858 / Num. obs: 11858 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 0.3896
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.83 / Num. unique all: 927 / Rsym value: 0.381 / % possible all: 62.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.78→7.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.07 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21801 617 4.9 %RANDOM
Rwork0.18953 ---
obs0.1909 11858 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.438 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.78→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms618 0 11 125 754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021643
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.171.951870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.224577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99723.21428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32915107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.791154
X-RAY DIFFRACTIONr_chiral_restr0.080.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02474
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2277
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6051.5395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.062629
X-RAY DIFFRACTIONr_scbond_it1.6253283
X-RAY DIFFRACTIONr_scangle_it2.6914.5240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 37 -
Rwork0.224 732 -
obs--86.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55581.131-0.47843.7525-0.60320.64730.0049-0.01310.0565-0.1549-0.04110.0519-0.0155-0.05430.0361-0.02240.00050.001-0.0290.0136-0.0611-15.69452.179-7.165
27.62470.60332.38318.6383.88571.7809-0.0020.20630.0149-0.15020.1451-0.9171-0.16790.2841-0.1431-0.0213-0.00950.037-0.02130.0254-0.0481-9.00349.574-7.606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 69
2X-RAY DIFFRACTION2B1 - 6

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