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- PDB-2da7: Solution structure of the homeobox domain of Zinc finger homeobox... -

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Basic information

Entry
Database: PDB / ID: 2da7
TitleSolution structure of the homeobox domain of Zinc finger homeobox protein 1b (Smad interacting protein 1)
ComponentsZinc finger homeobox protein 1b
KeywordsDNA BINDING PROTEIN / homeobox domain / three helices with the DNA binding helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of melanosome organization / positive regulation of myofibroblast contraction / regulation of blood-brain barrier permeability / phosphatase regulator activity / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / Regulation of CDH11 gene transcription / Formation of the anterior neural plate / melanocyte migration / response to oxygen-glucose deprivation ...regulation of melanosome organization / positive regulation of myofibroblast contraction / regulation of blood-brain barrier permeability / phosphatase regulator activity / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / Regulation of CDH11 gene transcription / Formation of the anterior neural plate / melanocyte migration / response to oxygen-glucose deprivation / positive regulation of melanocyte differentiation / myofibroblast differentiation / positive regulation of melanin biosynthetic process / developmental pigmentation / fibroblast activation / negative regulation of fibroblast migration / endothelial cell proliferation / stress fiber assembly / positive regulation of transforming growth factor beta receptor signaling pathway / pyroptotic inflammatory response / endothelial cell migration / astrocyte activation / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of canonical Wnt signaling pathway / nervous system development / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
: / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / Homeodomain / Homeobox domain / Zinc finger, C2H2 type / zinc finger / Homeodomain-like / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / Homeodomain / Homeobox domain / Zinc finger, C2H2 type / zinc finger / Homeodomain-like / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Zinc finger E-box-binding homeobox 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsOhnishi, S. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the homeobox domain of Zinc finger homeobox protein 1b (Smad interacting protein 1)
Authors: Ohnishi, S. / Kigawa, T. / Sato, M. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionDec 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
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
Revision 1.4May 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: Zinc finger homeobox protein 1b


Theoretical massNumber of molelcules
Total (without water)7,8851
Polymers7,8851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger homeobox protein 1b / Smad interacting protein 1 / SMADIP1


Mass: 7884.758 Da / Num. of mol.: 1 / Fragment: homeobox domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZFHX1B / Plasmid: P050404-18 / References: UniProt: O60315

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.2mM protein U-15N,13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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