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- PDB-2m1r: PHD domain of ING4 N214D mutant -

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Basic information

Entry
Database: PDB / ID: 2m1r
TitlePHD domain of ING4 N214D mutant
ComponentsInhibitor of growth protein 4
KeywordsGENE REGULATION / ING4 / PHD / TRANSCRIPTION
Function / homology
Function and homology information


regulation of DNA biosynthetic process / DNA replication-dependent chromatin disassembly / negative regulation of growth / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of cell cycle G2/M phase transition / intermediate filament cytoskeleton / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of cell cycle G2/M phase transition / intermediate filament cytoskeleton / protein acetylation / histone acetyltransferase complex / methylated histone binding / regulation of cell growth / HATs acetylate histones / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / positive regulation of apoptotic process / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / regulation of DNA-templated transcription / nucleoplasm / metal ion binding / 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)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsBlanco, F.J.
CitationJournal: Carcinogenesis / Year: 2010
Title: Functional impact of cancer-associated mutations in the tumor suppressor protein ING4.
Authors: Moreno, A. / Palacios, A. / Orgaz, J.L. / Jimenez, B. / Blanco, F.J. / Palmero, I.
History
DepositionDec 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Inhibitor of growth protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4573
Polymers7,3261
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Inhibitor of growth protein 4 / p29ING4


Mass: 7326.461 Da / Num. of mol.: 1 / Mutation: N214D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ING4, My036 / Variant: isoform 1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNL4
#2: Chemical ChemComp-ZN / ZINC ION / 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
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1313D 1H-15N NOESY
1413D 1H-15N TOCSY
1512D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 15N] ING4 PHD mutant N214D, 30 uM DSS, 1 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMING4 PHD mutant N214D-1[U-100% 15N]1
0.030 mMDSS-21
1 mMDTT-31
20 mMsodium phosphate-41
50 mMsodium chloride-51
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: 1 atm / 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
NameDeveloperClassification
XwinNMRBrukercollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: Simulated annealing combined with torsion angle dynamics. Iterative cycles of structure calculation and NOE assignment. Energy minimization in vacuo with implicit solvent (distance dependent dielecric constant)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 25 / Maximum upper distance constraint violation: 0.35 Å

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