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- PDB-7nbl: Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-d... -

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Basic information

Entry
Database: PDB / ID: 7nbl
TitleSolution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification
Components
  • DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3')
  • RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')
KeywordsDNA-RNA HYBRID / Fluorine modification / modified DNA / gemcitabine
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsCabrero, C. / Martin-Pintado, N. / Mazzini, S. / Gargallo, R. / Eritja, R. / Avino, A. / Gonzalez, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPRE2018-083173 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-89707-P Spain
CitationJournal: Chemistry / Year: 2021
Title: Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.
Authors: Cabrero, C. / Martin-Pintado, N. / Mazzini, S. / Gargallo, R. / Eritja, R. / Avino, A. / Gonzalez, C.
History
DepositionJan 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3')
B: RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,9902
Polymers4,9902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area850 Å2
ΔGint-1 kcal/mol
Surface area3230 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

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


Mass: 2447.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')


Mass: 2542.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
232isotropic12D 1H-1H COSY
242isotropic12D 1H-1H NOESY
252isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 90% H2O/10% D2ODiFs_Hybrid90% H2O/10% D2O
solution20.5 M DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 100% D2ODiFs_Hybrid_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 MDNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3')natural abundance1
0.5 MRNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')natural abundance1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
0.5 % v/vDSSnatural abundance1
0.5 MDNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3')natural abundance2
0.5 MRNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')natural abundance2
25 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
0.5 % v/vDSSnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1125 mMT571 atm278 K
2125 mMT2571 atm298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYGoddard & Knellerchemical shift assignment
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
3DNALu & Olsondata analysis
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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