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- PDB-2n2d: Structure of DNA G-quadruplex adopted by ALS and FTD related GGGG... -

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Basic information

Entry
Database: PDB / ID: 2n2d
TitleStructure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution
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 / antiparallel
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsBrcic, J. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution.
Authors: Brcic, J. / Plavec, J.
History
DepositionMay 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_software ...pdbx_entity_src_syn / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer ..._pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 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: 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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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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.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1131H-1H TOCSY
1311H-1H NOESY
1431H 1H DQF COSY
2521D 13C HSQC
1641D 15N HSQC
1731H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM dna, 120 mM potassium chloride, 20 mM potassium phosphate, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 MM DNA, 120 MM POTASSIUM CHLORIDE, 20 MM POTASSIUM PHOSPHATE, 100% D2O100% D2O
38%- 15, 8% 13 C N DNA 0.3-0.6 MM , 120 MM POTASSIUM CHLORIDE, 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O100% D2O
48%- 15 N DNA 0.3-0.6 MM , 120 MM POTASSIUM CHLORIDE, 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.5 mMdna-11
120 mMpotassium chloride-21
20 mMpotassium phosphate-31
0.5 mMdna-42
120 mMpotassium chloride-52
20 mMpotassium phosphate-62
mMdna-78% 13C, 8% 15 N0.3-0.62
120 mMpotassium chloride-82
20 mMpotassium phosphate-92
0.5 mMdna-103
120 mMpotassium chloride-113
20 mMpotassium phosphate-123
mMdna-138% 13C, 8% 15 N0.3-0.63
120 mMpotassium chloride-143
20 mMpotassium phosphate-153
mMdna-168% 15 N0.3-0.64
120 mMpotassium chloride-174
20 mMpotassium phosphate-184
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11407.2ambient 273 K
21407.2ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian Uniform NMR SystemVarianUniform NMR System8002

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Processing

NMR software
NameVersionDeveloperClassification
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
SparkyGoddardpeak picking
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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