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- PDB-7yvw: NMR determination of the 2:1 binding motif structure involving cy... -

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Basic information

Entry
Database: PDB / ID: 7yvw
TitleNMR determination of the 2:1 binding motif structure involving cytosine flipping out for the recognition of the CGG/CGG triad DNA
Components
  • DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3')
  • DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3')
KeywordsDNA / GG mismatch / drug / complex
Function / homologyChem-B2R / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsFuruita, K. / Yamada, T. / Sakurabayashi, S. / Nomura, M. / Kojima, C. / Nakatani, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26000007 Japan
Japan Society for the Promotion of Science (JSPS)19H00924 Japan
Japan Society for the Promotion of Science (JSPS)17K14516 Japan
Japan Society for the Promotion of Science (JSPS)19K05963 Japan
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: NMR determination of the 2:1 binding complex of naphthyridine carbamate dimer (NCD) and CGG/CGG triad in double-stranded DNA.
Authors: Yamada, T. / Furuita, K. / Sakurabayashi, S. / Nomura, M. / Kojima, C. / Nakatani, K.
History
DepositionAug 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1May 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(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*G)-3')
B: DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7544
Polymers6,7462
Non-polymers1,0072
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area4520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3382.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*CP*GP*GP*TP*TP*AP*G)-3')


Mass: 3364.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-B2R / 3-[3-[(7-methyl-1,8-naphthyridin-2-yl)carbamoyloxy]propylamino]propyl ~{N}-(7-methyl-1,8-naphthyridin-2-yl)carbamate / Naphthyridine Carbamate Dimer


Mass: 503.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29N7O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY (200 ms)
121isotropic22D 1H-13C HSQC
131isotropic12D 1H-31P HSQC
141isotropic12D DQF-COSY
151isotropic12D TOCSY
161isotropic12D NOESY (30 ms)

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Sample preparation

DetailsType: solution
Contents: 2.5 mM NCD-GG1, 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Label: unlabeled_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMNCD-GG1natural abundance1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 120 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: 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: 30

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