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- PDB-2pnx: The PHD finger of ING4 in complex with an H3K4Me3 histone peptide -

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Basic information

Entry
Database: PDB / ID: 2pnx
TitleThe PHD finger of ING4 in complex with an H3K4Me3 histone peptide
Components
  • H3K4Me3 peptide
  • Inhibitor of growth protein 4
KeywordsGENE REGULATION / protein-peptide complex / chromatin / zinc finger / histone
Function / homology
Function and homology information


DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / negative regulation of growth / intermediate filament cytoskeleton / histone H3K4me3 reader activity / regulation of cell cycle G2/M phase transition / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein acetylation / : / histone acetyltransferase complex ...DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / negative regulation of growth / intermediate filament cytoskeleton / histone H3K4me3 reader activity / regulation of cell cycle G2/M phase transition / positive regulation of DNA damage response, signal transduction by p53 class mediator / protein acetylation / : / histone acetyltransferase complex / regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / positive regulation of apoptotic process / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsChampagne, K.S. / Johnson, K. / Kutateladze, T.G.
CitationJournal: Mol.Cell / Year: 2009
Title: ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation
Authors: Hung, T. / Binda, O. / Champagne, K.S. / Kuo, A.J. / Johnson, K. / Chang, H.Y. / Simon, M.D. / Kutateladze, T.G. / Gozani, O.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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 4
B: H3K4Me3 peptide
C: Inhibitor of growth protein 4
D: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5558
Polymers15,2934
Non-polymers2624
Water2,342130
1
A: Inhibitor of growth protein 4
B: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7784
Polymers7,6472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Inhibitor of growth protein 4
D: H3K4Me3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7784
Polymers7,6472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.160, 68.160, 27.960
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Inhibitor of growth protein 4 / p29ING4


Mass: 6296.138 Da / Num. of mol.: 2 / Fragment: PHD domain, residues 194-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ING4 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)plyss / References: UniProt: Q9UNL4
#2: Protein/peptide H3K4Me3 peptide


Mass: 1350.568 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide H3K4me3 is naturally found in Homo sapiens (human).
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.04 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M sodium citrate tribasic dihydrate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.282, 1.283, 1.257
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 22, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2821
21.2831
31.2571
ReflectionResolution: 1.8→34.08 Å / Num. all: 23297 / Num. obs: 22220 / % possible obs: 98.8 % / Redundancy: 6.69 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2960 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→34.08 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1680 -RANDOM
Rwork0.199 ---
all-23297 --
obs-22220 95.2 %-
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 4 130 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.28

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