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- PDB-1wi3: Solution structure of the homeodomain of KIAA1034 protein -

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Basic information

Entry
Database: PDB / ID: 1wi3
TitleSolution structure of the homeodomain of KIAA1034 protein
ComponentsDNA-binding protein SATB2
KeywordsDNA BINDING PROTEIN / SATB2 / homeodomain / helix-turn-helix / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


embryonic skeletal system morphogenesis / embryonic pattern specification / cartilage development / osteoblast development / : / roof of mouth development / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...embryonic skeletal system morphogenesis / embryonic pattern specification / cartilage development / osteoblast development / : / roof of mouth development / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / nuclear matrix / histone deacetylase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / CUT domain ...Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / CUT domain / CUT domain / CUT domain profile. / CUT / 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
DNA-binding protein SATB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsIzumi, K. / Yoshida, M. / Hayashi, F. / Hatta, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Solution structure of the homeodomain of KIAA1034 protein
Authors: Izumi, K. / Yoshida, M. / Hayashi, F. / Hatta, R. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / 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 / _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: DNA-binding protein SATB2


Theoretical massNumber of molelcules
Total (without water)7,7551
Polymers7,7551
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, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein SATB2 / KIAA1034 protein / Special AT-rich sequence-binding protein 2 / two cut domains-containing ...KIAA1034 protein / Special AT-rich sequence-binding protein 2 / two cut domains-containing homeodomain protein / SATB2


Mass: 7754.691 Da / Num. of mol.: 1 / Fragment: Homeodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell free Synthesis / Gene: KAZUSA cDNA fh00753 / Plasmid: P040126-83 / References: UniProt: Q9UPW6

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.09mM 13C,15N-labeled protein; 20mM d-Tris-HCl buffer; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe2002045DELAGLIO,F.processing
NMRView5.0.4Johonson,B.A.data analysis
KUJIRA0.893Kobayashi,N.data analysis
CYANA1.0.7Guentert,P.structure solution
CYANA1.0.7Guentert,P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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