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- PDB-1du6: SOLUTION STRUCTURE OF THE TRUNCATED PBX HOMEODOMAIN -

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Basic information

Entry
Database: PDB / ID: 1du6
TitleSOLUTION STRUCTURE OF THE TRUNCATED PBX HOMEODOMAIN
ComponentsHOMEOBOX PROTEIN PBX1
KeywordsGENE REGULATION / homeodomain
Function / homology
Function and homology information


urogenital system development / natural killer cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / eye development / steroid biosynthetic process / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification ...urogenital system development / natural killer cell differentiation / proximal/distal pattern formation / embryonic skeletal system development / sex differentiation / eye development / steroid biosynthetic process / embryonic limb morphogenesis / embryonic hemopoiesis / anterior/posterior pattern specification / adrenal gland development / branching involved in ureteric bud morphogenesis / positive regulation of stem cell proliferation / negative regulation of neuron differentiation / regulation of ossification / neuron development / embryonic organ development / spleen development / positive regulation of G2/M transition of mitotic cell cycle / transcription corepressor binding / thymus development / stem cell proliferation / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / RNA polymerase II transcription regulator complex / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PBX, PBC domain / PBC domain / PBC domain profile. / : / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain ...PBX, PBC domain / PBC domain / PBC domain profile. / : / Homeobox KN domain / Homeobox KN domain / Homeobox, conserved site / 'Homeobox' domain signature. / '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
Pre-B-cell leukemia transcription factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / dynamical annealing
AuthorsSprules, T. / Green, N. / Featherstone, M. / Gehring, K.
CitationJournal: Biochemistry / Year: 2000
Title: Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides.
Authors: Sprules, T. / Green, N. / Featherstone, M. / Gehring, K.
History
DepositionJan 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 22, 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: HOMEOBOX PROTEIN PBX1


Theoretical massNumber of molelcules
Total (without water)7,4581
Polymers7,4581
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HOMEOBOX PROTEIN PBX1 / PBX1


Mass: 7458.345 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: PBX1 / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / References: UniProt: P41778

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
3332D NOESY
4442D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM PBX U-15N; 10 mM phosphate buffer; 1 mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
21 mM PBX U-15N,13C; 10 mM phosphate buffer; 1 mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
32 mM PBX; 1mM DTT; 90% H2O, 10% D2O90% H2O/10% D2O
44 mM PBX; 20 mM phosphate buffer; 1 mM DTT; 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
14.8ambient 303 K
24.8ambient 303 K
36ambient 303 K
46ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
Gifa4.2Pons, Malliavin, Delsucprocessing
CNS0.5Brungerstructure solution
XEASY1.3.13Bartels, Xia, Billeter, Guntert, Wuthrichdata analysis
CNS0.5Brungerrefinement
RefinementMethod: dynamical annealing / Software ordinal: 1
Details: 1338 restraints, 1268 NOE-derived distance constraints, 48 dihedral angle restraints, 22 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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