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- PDB-6lff: transcription factor SATB1 CUTr1 domain in complex with a phospho... -

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Basic information

Entry
Database: PDB / ID: 6lff
Titletranscription factor SATB1 CUTr1 domain in complex with a phosphorothioate DNA
Components
  • DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3')
  • DNA-binding protein SATB1
KeywordsTRANSCRIPTION/DNA / DNA-binding protein / DNA modification / Transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
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
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 / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / CUT domain ...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 / Ubiquitin-like (ULD) domain profile. / CUT repeat-like (CUTL) domain profile. / CUT domain / CUT domain / CUT domain profile. / CUT / Homeodomain / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-binding protein SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsAkutsu, Y. / Kubota, T. / Yamasaki, T. / Yamasaki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24570144 Japan
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Enhanced affinity of racemic phosphorothioate DNA with transcription factor SATB1 arising from diastereomer-specific hydrogen bonds and hydrophobic contacts.
Authors: Yamasaki, K. / Akutsu, Y. / Yamasaki, T. / Miyagishi, M. / Kubota, T.
History
DepositionDec 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein SATB1
B: DNA-binding protein SATB1
C: DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)29,3244
Polymers29,3244
Non-polymers00
Water1,24369
1
A: DNA-binding protein SATB1
C: DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,3723
Polymers18,3723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint2 kcal/mol
Surface area7800 Å2
MethodPISA
2
B: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)10,9521
Polymers10,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.320, 45.320, 97.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 10952.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SATB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01826
#2: DNA chain DNA (5'-D(*GP*(C7R)P*(PST)P*AP*AP*TP*AP*TP*AP*TP*GP*C)-3')


Mass: 3693.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*AP*TP*(AS)P*(PST)P*(AS)P*(PST)P*TP*AP*GP*C)-3')


Mass: 3725.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM Tris-HCl (pH 8.5), 20% polyethylene glycol monomethyl ether 550 (Sigma-Aldrich), 20% ethylene glycol, and 10 mM MgCl2

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→48.94 Å / Num. obs: 19724 / % possible obs: 93.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.6
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3103 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O4A

2o4a


Resolution: 1.79→19.63 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.882 / SU B: 3.538 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27122 1112 5.6 %RANDOM
Rwork0.22962 ---
obs0.23207 18596 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.79→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 471 0 69 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121943
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181575
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.5132728
X-RAY DIFFRACTIONr_angle_other_deg1.2691.8483681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6515162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33620.83396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30415261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0351519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0224.263654
X-RAY DIFFRACTIONr_mcbond_other2.0234.258653
X-RAY DIFFRACTIONr_mcangle_it3.2956.378814
X-RAY DIFFRACTIONr_mcangle_other3.2936.383815
X-RAY DIFFRACTIONr_scbond_it1.8333.9411289
X-RAY DIFFRACTIONr_scbond_other1.8323.9431290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0345.8381909
X-RAY DIFFRACTIONr_long_range_B_refined5.05243.2862330
X-RAY DIFFRACTIONr_long_range_B_other5.05143.3022329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.792→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 60 -
Rwork0.284 1487 -
obs--100 %

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