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- PDB-5oph: G-quadruplex structure of DNA oligonucleotide containing GGGGCC r... -

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Basic information

Entry
Database: PDB / ID: 5oph
TitleG-quadruplex structure of DNA oligonucleotide containing GGGGCC repeats linked to ALS and FTD
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3')
KeywordsDNA / G-quadruplex / Nucelar Magnetic Resonance / K+ solution / Antiparallel / Four G-quartets / Edgewise loops / Stacking / GGGGCC-repat / ALS and FTD / Neurodegenerative disorders / Repetitive Sequences / Nucleic Acid / 8Br-dG / modified residue
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBrcic, J. / Plavec, J.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: NMR structure of a G-quadruplex formed by four d(G4C2) repeats: insights into structural polymorphism.
Authors: Brcic, J. / Plavec, J.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jun 19, 2019Group: Data collection
Category: pdbx_nmr_spectrometer / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_spectrometer.details / _pdbx_nmr_spectrometer.manufacturer / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,0361
Polymers7,0361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area590 Å2
ΔGint5 kcal/mol
Surface area3860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 7036.323 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
111isotropic22D 1H-1H NOESY
192isotropic22D 1H-1H NOESY
122isotropic22D 1H-1H TOCSY
142isotropic12D DQF-COSY
152isotropic12D 1H-13C HSQC aliphatic
162isotropic12D 1H-13C HSQC aromatic
173isotropic11D 15N-edited HSQC
183isotropic11D 13C-edited HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11.0 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2Osl2_aqu_H2O90% H2O/10% D2O
solution20.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate, 100% D2Osl2_aqu_D2O100% D2O
solution30.3 mM one guanine in the sequence labeled 5% 15N and 13 C DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate, 90% H2O/10% D2Osamples_labeled90% H2O/10% D2O8% residue-specifically double 15 N, 13 C-labelled samples (15 distinct samples, for every DG in the molecule)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3')natural abundance1
30 mMpotassium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.4 mMDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3')natural abundance2
30 mMpotassium chloridenatural abundance2
20 mMpotassium phosphatenatural abundance2
0.3 mMDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3')one guanine in the sequence labeled 5% 15N and 13 C3
30 mMpotassium chloridenatural abundance3
20 mMpotassium phosphatenatural abundance3
Sample conditionsIonic strength: 53 mM / Label: 298 K / pH: 5.8 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian VNMRSVarianVNMRS6001Agilent-Varian
Varian VNMRSVarianVNMRS8002Agilent-Varian

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
VNMRVarianprocessing
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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