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- PDB-1v06: AXH domain of the transcription factor HBP1 from M.musculus -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1v06
TitleAXH domain of the transcription factor HBP1 from M.musculus
ComponentsHMG BOX-CONTAINING PROTEIN 1
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / TRANSCRIPTION FACTOR / PROTEIN-PROTEIN INTERACTION / NUCLEIC ACID BINDING / OB-FOLD / ATAXIN-1 HOMOLOGOUS / REPRESSOR / TRANSCRIPTION / TRANSCRIPTION REGULATION / WNT SIGNALING PATHWAY
Function / homology
Function and homology information


negative regulation of lipid transport / negative regulation of macrophage derived foam cell differentiation / negative regulation of reactive oxygen species biosynthetic process / Wnt signaling pathway / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleus
Similarity search - Function
HMG box-containing protein 1 / Ataxin, AXH domain / Ataxin, AXH domain superfamily / Ataxin-1 and HBP1 module (AXH) / AXH domain profile. / domain in Ataxins and HMG containing proteins / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
HMG box-containing protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsDe Chiara, C. / Kelly, G. / Pastore, A.
Citation
Journal: Structure / Year: 2005
Title: The Axh Domain Adopts Alternative Folds the Solution Structure of Hbp1 Axh.
Authors: De Chiara, C. / Menon, R.P. / Adinolfi, S. / De Boer, J. / Ktistaki, E. / Kelly, G. / Calder, L. / Kioussis, D. / Pastore, A.
#1: Journal: J.Biomol.NMR / Year: 2004
Title: Assignment of the 1H,13C, and 15N Resonances of the Axh Domain of the Transcription Factor Hbp1
Authors: De Chiara, C. / Kelly, G. / Frankiel, T.A. / Pastore, A.
#2: Journal: FEBS Lett. / Year: 2003
Title: The Axh Module:An Independently Folded Domain Common to Ataxin-1 and Hbp1
Authors: De Chiara, C. / Giannini, C. / Adinolfi, S. / Deboer, J. / Guida, S. / Ramos, A. / Jodice, C. / Kioussis, D. / Pastore, A.
History
DepositionMar 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HMG BOX-CONTAINING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)15,7761
Polymers15,7761
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 / 100LOWEST ENERGIES
RepresentativeModel #1

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Components

#1: Protein HMG BOX-CONTAINING PROTEIN 1 / HBP1 / HMG-BOX CONTAINING PROTEIN-1 / HMG BOX TRANSCRIPTION FACTOR 1 / HIGH MOBILITY GROUP BOX ...HBP1 / HMG-BOX CONTAINING PROTEIN-1 / HMG BOX TRANSCRIPTION FACTOR 1 / HIGH MOBILITY GROUP BOX TRANSCRIPTION FACTOR 1


Mass: 15775.749 Da / Num. of mol.: 1 / Fragment: AXH DOMAIN, RESIDUES 208-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R316
Sequence detailsTHE FOLLOWING N-TERMINAL RESIDUES FROM THE EXPRESSION SYSTEM TAG WERE NOT LOCATED IN THE EXPERIMENT: ...THE FOLLOWING N-TERMINAL RESIDUES FROM THE EXPRESSION SYSTEM TAG WERE NOT LOCATED IN THE EXPERIMENT: GLY ALA MET ALA

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121NOESY
NMR detailsText: STRUCTURAL RESTRAINTS WERE DERIVED FROM 13C- AND 15N-EDITED NOESY EXPERIMENTS AND J-COUPLINGS

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Sample preparation

DetailsContents: 0.7 MM 15N- OR 15N, 13C-LABELED PROTEIN, 20 MM TRIS-HCL, 10 MM NACL, 2 MM BETA-MERCAPTOETHANOL, 10% WATER/90% D2O
Sample conditionsIonic strength: 10 MM NACL / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA 1.2, CNS1.1NILGES, BRUNGER ET AL.refinement
NMRPipe1.7structure solution
XEASY1.2structure solution
ARIA1.2structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE EXPERIMENTALLY DETERMINED DISTANCE AND DIHEDRAL ANGLE RESTRAINTS WERE APPLIED IN A MIXED TORSION AND CARTESIAN DYNAMICS SIMULATED ANNEALING PROTOCOL. THE FINAL STRUCTURE ENSEMBLE WAS ...Details: THE EXPERIMENTALLY DETERMINED DISTANCE AND DIHEDRAL ANGLE RESTRAINTS WERE APPLIED IN A MIXED TORSION AND CARTESIAN DYNAMICS SIMULATED ANNEALING PROTOCOL. THE FINAL STRUCTURE ENSEMBLE WAS REFINED IN A SHELL OF WATER MOLECULES
NMR ensembleConformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 100 / Conformers submitted total number: 20

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