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- PDB-1ocp: SOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN -

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Entry
Database: PDB / ID: 1ocp
TitleSOLUTION STRUCTURE OF OCT3 POU-HOMEODOMAIN
ComponentsOCT-3
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


ectodermal cell fate commitment / response to benzoic acid / mesodermal cell fate commitment / HMG box domain binding / trophectodermal cell fate commitment / regulation of asymmetric cell division / endodermal cell fate specification / blastocyst growth / endodermal cell fate commitment / POU domain binding ...ectodermal cell fate commitment / response to benzoic acid / mesodermal cell fate commitment / HMG box domain binding / trophectodermal cell fate commitment / regulation of asymmetric cell division / endodermal cell fate specification / blastocyst growth / endodermal cell fate commitment / POU domain binding / germ-line stem cell population maintenance / negative regulation of calcium ion-dependent exocytosis / trophectodermal cell differentiation / female germ cell nucleus / germ cell nucleus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / cytokine binding / blastocyst development / somatic stem cell population maintenance / negative regulation of cell differentiation / cell fate commitment / positive regulation of transcription initiation by RNA polymerase II / response to retinoic acid / cis-regulatory region sequence-specific DNA binding / : / transcription repressor complex / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / telomere maintenance / cellular response to leukemia inhibitory factor / male germ cell nucleus / stem cell differentiation / chromatin DNA binding / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / DNA-binding transcription factor binding / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. ...POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
POU domain, class 5, transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsMorita, E.H. / Hayashi, F. / Shirakawa, M. / Kyogoku, Y.
Citation
Journal: Protein Sci. / Year: 1995
Title: Structure of the Oct-3 POU-Homeodomain in Solution, as Determined by Triple Resonance Heteronuclear Multidimensional NMR Spectroscopy
Authors: Morita, E.H. / Shirakawa, M. / Hayashi, F. / Imagawa, M. / Kyogoku, Y.
#1: Journal: FEBS Lett. / Year: 1993
Title: Secondary Structure of the Oct-3 POU Homeodomain as Determined by 1H-15N NMR Spectroscopy
Authors: Morita, E.H. / Shirakawa, M. / Hayashi, F. / Imagawa, K. / Kyogoku, Y.
History
DepositionFeb 21, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: OCT-3


Theoretical massNumber of molelcules
Total (without water)8,0291
Polymers8,0291
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 / -
Representative

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Components

#1: Protein OCT-3


Mass: 8029.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: T7 GENE 1 UNDER CONTROL OF THE / Plasmid: PAR2113 / Species (production host): Escherichia coli
Gene (production host): T7 GENE 1 UNDER CONTROL OF THE LAC UV5 PROMOTER
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20263

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 20

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