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- PDB-2k1j: Plan homeodomain finger of tumour supressor ING4 -

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Basic information

Entry
Database: PDB / ID: 2k1j
TitlePlan homeodomain finger of tumour supressor ING4
ComponentsInhibitor of growth protein 4
KeywordsGENE REGULATION / PHD / Zn / Acetylation / Alternative splicing / Anti-oncogene / Cell cycle / Coiled coil / Metal-binding / Nucleus / 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 cell cycle G2/M phase transition / intermediate filament cytoskeleton / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / protein acetylation / histone acetyltransferase complex / methylated histone binding / regulation of cell growth ...regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / regulation of cell cycle G2/M phase transition / intermediate filament cytoskeleton / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / protein acetylation / histone acetyltransferase complex / methylated histone binding / regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / positive regulation of apoptotic process / cell cycle / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / 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)
MethodSOLUTION NMR / molecular dynamics
AuthorsPalacios, A. / Garcia, P. / Padro, D. / Lopez-Hernandez, E. / Blanco, F.J.
CitationJournal: Febs Lett. / Year: 2006
Title: Solution structure and NMR characterization of the binding to methylated histone tails of the plant homeodomain finger of the tumour suppressor ING4.
Authors: Palacios, A. / Garcia, P. / Padro, D. / Lopez-Hernandez, E. / Martin, I. / Blanco, F.J.
History
DepositionMar 5, 2008Deposition site: BMRB / Processing site: RCSB
SupersessionApr 15, 2008ID: 2JMQ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of growth protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4563
Polymers7,3251
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Inhibitor of growth protein 4 / p29ING4


Mass: 7325.476 Da / Num. of mol.: 1 / Fragment: PHD-type zinc-finger, UNP residues 188-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ING4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UNL4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D H(CCO)NH
1633D HNHA
1733D HNHB
1833D 1H-15N NOESY
1933D 1H-15N TOCSY
11013D 1H-13C NOESY
11123D (H)CCH-TOCSY
11213D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-95% 13C; U-90% 15N] Plant Homeodomain of ING4, 95% H2O, 5% D2O95% H2O/5% D2O
21.2 mM [U-95% 13C; U-90% 15N] Plant Homeodomain of ING4, 100% D2O100% D2O
30.9 mM [U-90% 15N] Plant Homeodomain of ING4, 95% H2O, 5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMPlant Homeodomain of ING4[U-95% 13C; U-90% 15N]1
1.2 mMPlant Homeodomain of ING4[U-95% 13C; U-90% 15N]2
0.9 mMPlant Homeodomain of ING4[U-90% 15N]3
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber7Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollrefinement
NMRViewJohnson, One Moon Scientificdata analysis
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 8 / Protein phi angle constraints total count: 30 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 25

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