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- PDB-8bm4: Hairpin adopted by modified oligonucleotide A32_mod found in the ... -

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Basic information

Entry
Database: PDB / ID: 8bm4
TitleHairpin adopted by modified oligonucleotide A32_mod found in the promoter of AUTS2 gene.
ComponentsA32_mod
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: A32_mod


Theoretical massNumber of molelcules
Total (without water)9,9431
Polymers9,9431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, NMR data are in perfect agreement with hairpin formation.
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 A32_mod


Mass: 9943.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
112isotropic12D NOESY
321isotropic12D NOESY
331isotropic12D DQF-COSY
341isotropic22D 1H-31P CT-COSY
251isotropic12D NOESY
261isotropic12D DQF-COSY
373isotropic12D 1H-13C HSQC
384isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.6 mM DNA, 20 mM potassium phosphate, 100% D2OA32_mod_1 0.6mM DNA 20mM KPi buffer pH 7.2A32_mod_1100% D2O
solution20.6 mM DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA32_mod_1 0.6mM DNA 20mM KPi buffer pH 7.2A32_mod_290% H2O/10% D2O
solution30.4 mM Residue-specific, 10% 13C/15N DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA32_1 0.4mM DNA 20mM KPi buffer pH 7.2 Residue-specific labelling.A32_190% H2O/10% D2O
solution40.6 mM 10 residues, 10% 13C/15N DNA, 20 mM potassium phosphate, 90% H2O/10% D2OA32_1 0.6mM DNA 20mM KPi buffer pH 7.2 Selected adenines labelled.A32_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMDNAnatural abundance1
20 mMpotassium phosphatenatural abundance1
0.6 mMDNAnatural abundance2
20 mMpotassium phosphatenatural abundance2
0.4 mMDNAResidue-specific, 10% 13C/15N3
20 mMpotassium phosphatenatural abundance3
0.6 mMDNA10 residues, 10% 13C/15N4
20 mMpotassium phosphatenatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM273K7.21 atm273 K
220 mM298K7.21 atm298 K
320 mM318K7.21 atm318 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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