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- PDB-6dm7: NMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG) -

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Basic information

Entry
Database: PDB / ID: 6dm7
TitleNMR structure for Sp1 transcription factor duplex 5'-d(GGGGCGGGG)
Components
  • DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*G)-3')
KeywordsDNA / Sp1 Consensus Sequence
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDavis, E.V. / Hennig, M. / Arya, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM097917 United States
CitationJournal: To Be Published
Title: An NMR Structure Determination and Analysis of Four Sp1 Consensus Sequences
Authors: Davis, E.V. / Hennig, M. / Arya, D.P.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,4762
Polymers5,4762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: U.V. Thermal denaturation, CD spectroscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area870 Å2
ΔGint-8 kcal/mol
Surface area3640 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*CP*GP*GP*GP*G)-3')


Mass: 2877.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain A / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*CP*CP*CP*GP*CP*CP*CP*C)-3')


Mass: 2597.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Watson-Crick DNA duplex chain B / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D DQF-COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-1H NOESY
152isotropic32D 1H-1H NOESY
161isotropic32D ECOSY
171isotropic22D PhCOSY
181isotropic22D PhTOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM DNA, 25 mM sodium chloride, 5 mM Na Phoshate, 0.5 mM EDTA, 100% D2Oequal molar eq. d(GGGGCGGGG).d(CCCCGCCCC) 100% D2O 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0non-exchange100% D2O
solution2680 uM DNA, 25 mM sodium chloride, 5 mM Na Phosphate, 0.5 mM EDTA, 90% H2O/10% D2Oequal molar eq. d(GGGGCGGGG).d(CCCCGCCCC) 90% H2O /10% D2O 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0exchange90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDNAnatural abundance1
25 mMsodium chloridenatural abundance1
5 mMNa Phoshatenatural abundance1
0.5 mMEDTAnatural abundance1
680 uMDNAnatural abundance2
25 mMsodium chloridenatural abundance2
5 mMNa Phosphatenatural abundance2
0.5 mMEDTAnatural abundance2
Sample conditionsDetails: equal molar eq. d(GGGGCGGGG).d(CCCCGCCCC) 100% D2O 25 mM NaCl, 5.0 mM Na Phosphate 0.5 mM EDTA pH 7.0
Ionic strength: 30 mM Na+ mM / Label: non-exchange / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCE IIIBrukerAVANCE III8503
Bruker AVANCE IIBrukerAVANCE II6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
3DNALudata analysis
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 214 NOE distance constraints, 54 hydrogen distance restraints, 48 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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