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- PDB-8cok: Structural analysis of ING3 protein and its binding to histone H3 -

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Basic information

Entry
Database: PDB / ID: 8cok
TitleStructural analysis of ING3 protein and its binding to histone H3
ComponentsInhibitor of growth protein 3
KeywordsDNA BINDING PROTEIN / ING3 / histone H3 / PHD / protein structure / molecular recognition
Function / homology
Function and homology information


histone H2A acetyltransferase activity / : / : / : / histone H4K12 acetyltransferase activity / piccolo histone acetyltransferase complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / Swr1 complex ...histone H2A acetyltransferase activity / : / : / : / histone H4K12 acetyltransferase activity / piccolo histone acetyltransferase complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / Swr1 complex / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / methylated histone binding / nucleosome / chromatin organization / regulation of cell cycle / positive regulation of apoptotic process / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
ING3, 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 finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type ...ING3, 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 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
Similarity search - Domain/homology
Inhibitor of growth protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsFerreras-Gutierrez, M. / Medrano, F.J. / Blanco, F.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-113225GB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural analysis of ING3 protein and histone H3 binding.
Authors: Ferreras-Gutierrez, M. / Chaves-Arquero, B. / Gonzalez-Magana, A. / Merino, N. / Amusategui-Mateu, I. / Huecas, S. / Medrano, F.J. / Blanco, F.J.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of growth protein 3
B: Inhibitor of growth protein 3


Theoretical massNumber of molelcules
Total (without water)25,2792
Polymers25,2792
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, SEC-MALS, NMR spectra, Thermal denaturatuion by CD
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-38 kcal/mol
Surface area12630 Å2
Unit cell
Length a, b, c (Å)149.394, 149.394, 149.394
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2

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Components

#1: Protein Inhibitor of growth protein 3


Mass: 12639.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ing3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q498T3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate-citrate buffer at pH 4.2, 10 % 2-propanol and 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2022 / Details: KB focusing mirrors
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 2.91→74.69 Å / Num. obs: 6277 / % possible obs: 95.7 % / Redundancy: 73.9 % / Biso Wilson estimate: 126.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.011 / Rrim(I) all: 0.081 / Net I/σ(I): 41.4
Reflection shellResolution: 2.91→3 Å / Redundancy: 80.3 % / Rmerge(I) obs: 6.609 / Num. unique obs: 319 / CC1/2: 0.565 / Rpim(I) all: 0.738 / Rrim(I) all: 6.651 / % possible all: 55.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→60.99 Å / SU ML: 0.5913 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.4551
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3154 627 9.99 %
Rwork0.2696 5649 -
obs0.2745 6276 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.73 Å2
Refinement stepCycle: LAST / Resolution: 2.91→60.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 0 4 1706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951726
X-RAY DIFFRACTIONf_angle_d1.312309
X-RAY DIFFRACTIONf_chiral_restr0.0586239
X-RAY DIFFRACTIONf_plane_restr0.0143306
X-RAY DIFFRACTIONf_dihedral_angle_d5.1355221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.20.54161310.46191181X-RAY DIFFRACTION82.15
3.2-3.660.43491600.35911440X-RAY DIFFRACTION100
3.67-4.610.33531620.29341461X-RAY DIFFRACTION100
4.62-60.990.27611740.23451567X-RAY DIFFRACTION99.94

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