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- PDB-2mw8: Solution structure of SATB1 homeodomain -

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Basic information

Entry
Database: PDB / ID: 2mw8
TitleSolution structure of SATB1 homeodomain
ComponentsDNA-binding protein SATB1
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body ...Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / chromatin organization / double-stranded DNA binding / sequence-specific DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
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 SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYamasaki, K. / Yamasaki, T.
CitationJournal: To be Published
Title: Solution structure of SATB1 homeodomain
Authors: Yamasaki, K. / Yamasaki, T.
History
DepositionOct 31, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)8,3171
Polymers8,3171
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein SATB1 / Special AT-rich sequence-binding protein 1


Mass: 8316.596 Da / Num. of mol.: 1 / Fragment: UNP residues 641-707
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SATB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01826

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2222D 1H-15N HSQC
2323D 1H-15N NOESY
2423D 1H-15N TOCSY
2532D 1H-1H NOESY
2632D DQF-COSY
2732D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-15N] SATB1 homeodomain-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 0.5 mM DSS-4, 95% H2O/5% D2O95% H2O/5% D2O
20.7-1.2 mM [U-15N] SATB1 homeodomain-5, 50 mM sodium phosphate-6, 200 mM sodium chloride-7, 0.5 mM DSS-8, 95% H2O/5% D2O95% H2O/5% D2O
30.7-1.2 mM SATB1 homeodomain-9, 50 mM sodium phosphate-10, 200 mM sodium chloride-11, 0.5 mM DSS-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.3 mMSATB1 homeodomain-1[U-15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
0.5 mMDSS-41
mMSATB1 homeodomain-5[U-15N]0.7-1.22
50 mMsodium phosphate-62
200 mMsodium chloride-72
0.5 mMDSS-82
mMSATB1 homeodomain-90.7-1.23
50 mMsodium phosphate-103
200 mMsodium chloride-113
0.5 mMDSS-123
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 5.5 ambient 298 K
20.25 5.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
FelixAccelrys Software Inc.data analysis
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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