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- PDB-6a7y: Solution structure of an intermolecular leaped V-shape G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 6a7y
TitleSolution structure of an intermolecular leaped V-shape G-quadruplex
Components
  • DNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
  • DNA (5'-D(*TP*GP*GP*GP*GP*A)-3')
KeywordsDNA / G-quadruplex / V-shape
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesSterkiella nova (eukaryote)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsWan, C.J. / Zhang, N.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)31600621 China
National Natural Science Foundation of China21372223 China
National Natural Science Foundation of ChinaU1232145 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe.
Authors: Wan, C. / Fu, W. / Jing, H. / Zhang, N.
History
DepositionJul 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
B: DNA (5'-D(*TP*GP*GP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)7,5702
Polymers7,5702
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area4270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5680.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterkiella nova (eukaryote) / Production host: synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*GP*GP*GP*GP*A)-3')


Mass: 1889.265 Da / Num. of mol.: 1 / Mutation: T24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterkiella nova (eukaryote) / Production host: synthetic construct (others)
Sequence detailsChain B has a T-to-A mutated sequence. The original sequence is d(TGGGGT).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-13C HSQC
152isotropic12D DQF-COSY
161isotropic12D 1H-13C HMBC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM DNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'), 2 mM DNA (5'-D(*TP*GP*GP*GP*GP*A)-3'), 90% H2O/10% D2Osample_190% H2O/10% D2O
solution22 mM DNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'), 2 mM DNA (5'-D(*TP*GP*GP*GP*GP*A)-3'), 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMDNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')natural abundance1
2 mMDNA (5'-D(*TP*GP*GP*GP*GP*A)-3')natural abundance1
2 mMDNA (5'-D(*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')natural abundance2
2 mMDNA (5'-D(*TP*GP*GP*GP*GP*A)-3')natural abundance2
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AnalysisCCPNdata analysis
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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