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- PDB-3c6w: Crystal structure of the ING5 PHD finger in complex with H3K4me3 ... -

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Basic information

Entry
Database: PDB / ID: 3c6w
TitleCrystal structure of the ING5 PHD finger in complex with H3K4me3 peptide
Components
  • H3K4me3 histone peptide
  • Inhibitor of growth protein 5
KeywordsMETAL BINDING PROTEIN / Chromatin / PHD / ING / epigenetics / histone / Alternative splicing / Metal-binding / Phosphoprotein / Zinc / Zinc-finger
Function / homology
Function and homology information


regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / protein acetylation / regulation of DNA replication / histone acetyltransferase complex / negative regulation of fibroblast proliferation ...regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / protein acetylation / regulation of DNA replication / histone acetyltransferase complex / negative regulation of fibroblast proliferation / Regulation of TP53 Activity through Acetylation / methylated histone binding / regulation of cell growth / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / HATs acetylate histones / fibroblast proliferation / regulation of cell cycle / positive regulation of apoptotic process / negative regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding
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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsChampagne, K.S. / Pena, P.V. / Johnson, K. / Kutateladze, T.G.
CitationJournal: Proteins / Year: 2008
Title: The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide.
Authors: Champagne, K.S. / Saksouk, N. / Pena, P.V. / Johnson, K. / Ullah, M. / Yang, X.J. / Cote, J. / Kutateladze, T.G.
History
DepositionFeb 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of growth protein 5
B: H3K4me3 histone peptide
C: Inhibitor of growth protein 5
D: H3K4me3 histone peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5488
Polymers16,2874
Non-polymers2624
Water2,468137
1
A: Inhibitor of growth protein 5
B: H3K4me3 histone peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2744
Polymers8,1432
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
MethodPISA
2
C: Inhibitor of growth protein 5
D: H3K4me3 histone peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2744
Polymers8,1432
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.140, 68.140, 28.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biomolecule is a monomer with a bound peptide

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Components

#1: Protein Inhibitor of growth protein 5 / p28ING5


Mass: 6792.862 Da / Num. of mol.: 2 / Fragment: UNP residues 184-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ING5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYH8
#2: Protein/peptide H3K4me3 histone peptide


Mass: 1350.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic H3K4me3 histone peptide
#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.: 137 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Sodium Citrate, 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: 1.2574, 1.28304, 1.28264
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 22, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25741
21.283041
31.282641
ReflectionResolution: 1.75→34 Å / Num. obs: 13176 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.95 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.23 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
SOLVEphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→34 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.199 1888 random
Rwork0.186 --
obs0.186 12981 -
all-25634 -
Displacement parametersBiso mean: 20.3814 Å2
Baniso -1Baniso -2Baniso -3
1-0.159 Å20 Å20 Å2
2--0.159 Å20 Å2
3----0.318 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-1.75 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.75→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 4 137 1116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007403
X-RAY DIFFRACTIONc_angle_deg1.33696
X-RAY DIFFRACTIONc_dihedral_angle_d23.297
X-RAY DIFFRACTIONc_improper_angle_d1.51967
LS refinement shellResolution: 1.75→1.81 Å
RfactorNum. reflection
Rfree0.246 157
Rwork0.211 -
obs-1971

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