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- PDB-8bm7: Hairpin adopted by oligonucleotide A38 found in the promoter of A... -

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Basic information

Entry
Database: PDB / ID: 8bm7
TitleHairpin adopted by oligonucleotide A38 found in the promoter of AUTS2 gene.
ComponentsA38
KeywordsDNA / AUTS2 / sheared GA / CGAG block / hairpin
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsNovotny, A.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyZ1-3192 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural polymorphism driven by a register shift in a CGAG-rich region found in the promoter of the neurodevelopmental regulator AUTS2 gene.
Authors: Novotny, A. / Plavec, J. / Kocman, V.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 19, 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: A38


Theoretical massNumber of molelcules
Total (without water)11,8731
Polymers11,8731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, A38 oligonucleotide migrates a bit faster than a DNA duplex containing 20 base pairs.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain A38


Mass: 11872.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / 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 NOESY
121isotropic12D DQF-COSY
131isotropic22D 1H-31P CT-COSY
242isotropic12D NOESY
153isotropic22D 1H-13C HSQC
164isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.2 mM DNA, 20 mM potassium phosphate, 100% D2OA38_D2O 1.2mM DNA 20mM KPi buffer pH7.2A38_1100% D2O
solution21.2 mM DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA38_H2O 1.2mM DNA 20mM KPi buffer pH7.2A38_290% H2O/10% D2O
solution30.6 mM Residue-specific, 10% 13C/15N DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA38_H2O 0.6mM DNA 20mM KPi buffer pH7.2A38_390% H2O/10% D2O
solution40.6 mM 10 residues, 10% 13C/15N DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA38_H2O 0.6mM DNA 20mM KPi buffer pH7.2A38_490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMDNAnatural abundance1
20 mMpotassium phosphatenatural abundance1
1.2 mMDNAnatural abundance2
20 mMpotassium phosphatenatural abundance2
0.6 mMDNAResidue-specific, 10% 13C/15N3
20 mMpotassium phosphatenatural abundance3
0.6 mMDNA10 residues, 10% 13C/15N4
20 mMpotassium phosphatenatural abundance4
Sample conditions

Ionic strength: 20 mM / Ionic strength err: 2 / pH: 7.2 / PH err: 0.1 / Pressure: 1 atm

Conditions-IDLabelTemperature (K)
11298 K
22278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE NEOBrukerAVANCE NEO8001HCN cryoprobe
Bruker AVANCE NEOBrukerAVANCE NEO6002HCNP cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madisonchemical shift assignment
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madisondata analysis
Amber2020Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4 / Details: See attached restraint files.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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