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- PDB-7atz: G-quadruplex with V-shaped loop from the first repeat of KCNN4 mi... -

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Basic information

Entry
Database: PDB / ID: 7atz
TitleG-quadruplex with V-shaped loop from the first repeat of KCNN4 minisatellite
ComponentsDNA (5'-D(*GP*GP*TP*CP*TP*GP*AP*GP*GP*GP*AP*GP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-Quadruplex / V-loop
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsVianney, Y.M. / Weisz, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 292/138-1 Germany
CitationJournal: Biochemistry / Year: 2021
Title: First Tandem Repeat of a Potassium Channel KCNN4 Minisatellite Folds into a V-Loop G-Quadruplex Structure.
Authors: Vianney, Y.M. / Weisz, K.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 12, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*CP*TP*GP*AP*GP*GP*GP*AP*GP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,2991
Polymers7,2991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3890 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*GP*TP*CP*TP*GP*AP*GP*GP*GP*AP*GP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*T)-3')


Mass: 7298.680 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is derived from first intron of the KCNN4 gene in human
Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aromatic
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HMBC
142isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.9 mM No DNA, 90% H2O/10% D2OSample was dissolved in 90% 10 mM potassium phosphate buffer + 10 % D2OKCNN4-1A-dG13-3'T90% H2O/10% D2O
solution20.9 mM No DNA, 100% D2O10 mM potassium phosphate bufferKCNN4-1A-dG13-3'T_EX100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMDNANo1
0.9 mMDNANo2
Sample conditionsDetails: 10 mM K+, 25 dC / Ionic strength: 10 mM / Label: conditions1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
TopSpin4.0.7Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNdata analysis
X-PLOR NIH3.0.3Schwieters, Kuszewski, Tjandra and Clorerefinement
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing4
simulated annealing5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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