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- PDB-2g6q: Crystal structure of ING2 PHD finger in complex with H3K4Me3 peptide -

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Basic information

Entry
Database: PDB / ID: 2g6q
TitleCrystal structure of ING2 PHD finger in complex with H3K4Me3 peptide
Components
  • H3K4Me3 peptide
  • Inhibitor of growth protein 2
KeywordsGENE REGULATION / APOPTOSIS / protein-peptide complex / PHD finger
Function / homology
Function and homology information


PI5P Regulates TP53 Acetylation / male germ-line stem cell asymmetric division / CCAAT-binding factor complex / SUMOylation of transcription cofactors / flagellated sperm motility / negative regulation of stem cell population maintenance / histone deacetylase regulator activity / negative regulation of gene expression, epigenetic / Sin3-type complex / positive regulation of stem cell population maintenance ...PI5P Regulates TP53 Acetylation / male germ-line stem cell asymmetric division / CCAAT-binding factor complex / SUMOylation of transcription cofactors / flagellated sperm motility / negative regulation of stem cell population maintenance / histone deacetylase regulator activity / negative regulation of gene expression, epigenetic / Sin3-type complex / positive regulation of stem cell population maintenance / seminiferous tubule development / male meiosis I / positive regulation of transforming growth factor beta receptor signaling pathway / spermatid development / negative regulation of apoptotic signaling pathway / methylated histone binding / histone reader activity / phosphatidylinositol binding / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / spermatogenesis / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane
Similarity search - Function
ING2, PHD domain / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...ING2, PHD domain / Inhibitor of growth protein, N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / Inhibitor of growth proteins N-terminal histone-binding / ING family / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Inhibitor of growth protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPena, P.V. / Zhao, R. / Kutateladze, T.G.
CitationJournal: Nature / Year: 2006
Title: Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2.
Authors: Pena, P.V. / Davrazou, F. / Shi, X. / Walter, K.L. / Verkhusha, V.V. / Gozani, O. / Zhao, R. / Kutateladze, T.G.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2013Group: Structure summary
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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: Inhibitor of growth protein 2
B: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6204
Polymers8,4902
Non-polymers1312
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.176, 49.176, 52.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Inhibitor of growth protein 2 / p33ING2 / Inhibitor of growth 1-like protein / ING1Lp / p32


Mass: 7139.000 Da / Num. of mol.: 1 / Fragment: PHD domain (residues 204-263)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ING2, ING1L / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9ESK4
#2: Protein/peptide H3K4Me3 peptide


Mass: 1350.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: H3K4Me3 is chemically synthesized
#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.: 32 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 22% PEGMME2K, 0.01M NiCl2(6H2O), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 5116 / % possible obs: 97 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 51
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 18.5 / Num. unique all: 407 / % possible all: 79.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1WES

1wes


Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2313 527 random
Rwork0.2233 --
all-5243 -
obs-5074 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 2 32 522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.08
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.2388 55
Rwork0.2345 -
obs-348

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