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- PDB-2e1o: Solution structure of RSGI RUH-028, a homeobox domain from human cDNA -

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Basic information

Entry
Database: PDB / ID: 2e1o
TitleSolution structure of RSGI RUH-028, a homeobox domain from human cDNA
ComponentsHomeobox protein PRH
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DNA binding protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of leukocyte proliferation / DNA-binding transcription factor binding => GO:0140297 / negative regulation of transcription by transcription factor localization / eukaryotic initiation factor 4E binding / DNA conformation change / chromatin => GO:0000785 / negative regulation of transcription by competitive promoter binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / poly(A)+ mRNA export from nucleus / DNA binding, bending ...regulation of leukocyte proliferation / DNA-binding transcription factor binding => GO:0140297 / negative regulation of transcription by transcription factor localization / eukaryotic initiation factor 4E binding / DNA conformation change / chromatin => GO:0000785 / negative regulation of transcription by competitive promoter binding / negative regulation of cyclin-dependent protein serine/threonine kinase activity / poly(A)+ mRNA export from nucleus / DNA binding, bending / anterior/posterior pattern specification / negative regulation of vascular endothelial growth factor receptor signaling pathway / transcription factor binding / protein localization to nucleus / positive regulation of Wnt signaling pathway / mRNA export from nucleus / TBP-class protein binding / negative regulation of angiogenesis / B cell differentiation / protein-DNA complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to peptide hormone / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / positive regulation of canonical Wnt signaling pathway / sequence-specific DNA binding / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hematopoietically-expressed homeobox protein HHEX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNakamura, A. / Ohnishi, S. / Abe, T. / Nameki, N. / Tochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / Kawaii, S. / Hirota, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-028, a homeobox domain from human cDNA
Authors: Nakamura, A. / Ohnishi, S. / Abe, T. / Nameki, N. / Tochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / Kawaii, S. / Hirota, H.
History
DepositionOct 27, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 14, 2006ID: 1WQI
Revision 1.0Nov 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox protein PRH


Theoretical massNumber of molelcules
Total (without water)8,0591
Polymers8,0591
Non-polymers00
Water0
1


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

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Components

#1: Protein Homeobox protein PRH / / Hematopoietically expressed homeobox / Homeobox protein HEX


Mass: 8059.108 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: HHEX, HEX, PRH, PRHX / Plasmid: P040315-39 / Production host: Cell free synthesis / References: UniProt: Q03014

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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: 0.92mM RSGI RUH-028 U-15N,13C, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 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
XwinNMR3.6Brukercollection
NMRPipe2003.316.09.03Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA2.0.172Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy and target function
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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