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- PDB-2l1p: NMR solution structure of the N-terminal domain of DNA-binding pr... -

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Basic information

Entry
Database: PDB / ID: 2l1p
TitleNMR solution structure of the N-terminal domain of DNA-binding protein SATB1 from Homo sapiens: Northeast Structural Genomics Target HR4435B(179-250)
ComponentsDNA-binding protein SATB1
KeywordsDNA BINDING PROTEIN / PSI-Biology / NESG / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
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, CULT 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. ...SATB, CULT 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 / '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-binding protein SATB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSwapna, G.V.T. / Montelione, A.F. / Shastry, R. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of the N-terminal domain of DNA-binding protein SATB1 from Homo sapiens: Northeast Structural Genomics Target HR4435B(179-250)
Authors: Swapna, G.V.T. / Montelione, A.F. / Shastry, R. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T.
History
DepositionAug 2, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_spectrometer.model / _struct_ref_seq_dif.details

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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)9,6991
Polymers9,6991
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 / 150structures 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: 9699.128 Da / Num. of mol.: 1 / Fragment: Sequence database residues 179-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SATB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / 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
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D HNCO
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 1H-15N HSQC
11112D 1H-13C HSQC
NMR detailsText: Data acquisition on B600 was performed using 35 uL of 1.08mM sample and a 1.7mm microcryoprobe.

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Sample preparation

DetailsContents: 1.08 mM [U-100% 13C; U-100% 15N] HR4435B, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.08 mM / Component: HR4435B-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 5mM CaCl2, 100mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using Autoassign. Sidechain assignments were completed manually. Automated ...Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using Autoassign. Sidechain assignments were completed manually. Automated NOESY assignments were made using AutoStructure and structure solution was obtained using AutoStructure and CYANA-2.1. 150 structures were calculated and 20 best structures were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. The structure calculations were done including the N-terminal 6xHis tag. Resonance assignments were validated using AVS validation software. Final quality scores were determined using PSVS software. Ordered residues are defined as:11-13,18-54,62-77 . RMSD(ordered residuesall backbone aatoms 0.9A; All heavy atoms 1.4A; Ramachandran Statistics for all ordered residues: Most favoured 94.6%, additionally allowed region: 5.4%; Procheck scores for all ordered residues (Raw/Z) phi-psi 0.09/0.67; All dihedral angles 0.04/0.24; MolProbity clash score (Raw/Z) 13.00/-0.71. RPF scores for the goodness of fir of the structure to the NMR data: recall:0.933; Precision 0.918; F-measure 0.926 and final DP score: 0.768
NMR constraintsNOE constraints total: 712 / NOE intraresidue total count: 80 / NOE long range total count: 151 / NOE medium range total count: 236 / NOE sequential total count: 245
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.1 Å
NMR ensemble rmsDistance rms dev: 0 Å

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