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- PDB-5me8: N-terminal domain of the human tumor suppressor ING5 -

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Basic information

Entry
Database: PDB / ID: 5me8
TitleN-terminal domain of the human tumor suppressor ING5
ComponentsInhibitor of growth protein 5
KeywordsTRANSCRIPTION / tumor suppressor / ING5 / asymmetric dimer
Function / homology
Function and homology information


DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / 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 ...DNA replication-dependent chromatin disassembly / regulation of DNA biosynthetic process / 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 / positive regulation of apoptotic signaling pathway / regulation of cell growth / 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
Helix Hairpins - #1740 / 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 / Helix Hairpins / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Helix non-globular ...Helix Hairpins - #1740 / 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 / Helix Hairpins / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Helix non-globular / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Special / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Inhibitor of growth protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRoversi, P. / Blanco, F.J. / Rojas, A.L. / Buitrago, J.A.R.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: The Tumor Suppressor ING5 Is a Dimeric, Bivalent Recognition Molecule of the Histone H3K4me3 Mark.
Authors: Ormaza, G. / Rodriguez, J.A. / Ibanez de Opakua, A. / Merino, N. / Villate, M. / Gorrono, I. / Rabano, M. / Palmero, I. / Vilaseca, M. / Kypta, R. / Vivanco, M.D.M. / Rojas, A.L. / Blanco, F.J.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inhibitor of growth protein 5
B: Inhibitor of growth protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,79511
Polymers25,1252
Non-polymers6719
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-6 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.630, 135.630, 96.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Inhibitor of growth protein 5 / p28ING5


Mass: 12562.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GA is cloning artefact / Source: (gene. exp.) Homo sapiens (human) / Gene: ING5 / Plasmid: pET11d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WYH8
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 5.11 Å3/Da / Density % sol: 75.92 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 22 % MPD, 0.1 M MES pH 6.5, 5% PEG 3350

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.978861 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978861 Å / Relative weight: 1
ReflectionResolution: 3.2→44.7 Å / Num. obs: 9086 / % possible obs: 99.89 % / Redundancy: 7.6 % / Biso Wilson estimate: 109.52 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 47.54
Reflection shellResolution: 3.2→3.39 Å / Redundancy: 35 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 6.2 / CC1/2: 0.972 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BKC, 4AFL

2bkc

4afl


Resolution: 3.2→44.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.775 / SU Rfree Blow DPI: 0.358 / Details: TLS refinement with one set of TLS per chain
RfactorNum. reflection% reflectionSelection details
Rfree0.248 433 4.77 %RANDOM
Rwork0.211 ---
obs0.213 9076 99.9 %-
Displacement parametersBiso mean: 105.53 Å2
Baniso -1Baniso -2Baniso -3
1-3.2505 Å20 Å20 Å2
2--3.2505 Å20 Å2
3----6.501 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 3.2→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 44 13 1815
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093647HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.996575HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d865SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes507HARMONIC5
X-RAY DIFFRACTIONt_it3647HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion238SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3998SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.281 123 4.9 %
Rwork0.234 2389 -
all0.236 2512 -
obs--99.8 %
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)
13.29464.80863.09178.66735.81934.9470.0222-0.15910.0470.8211-0.22180.15740.97550.18050.19960.05640.01180.0834-0.1178-0.0443-0.2778-57.293526.4185-29.7313
22.32580.4961-1.92272.2409-0.62337.4564-0.268-0.2329-0.28180.00010.13110.14430.85310.49490.137-0.307-0.0893-0.0635-0.25650.0932-0.2391-42.775841.0348-8.2089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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