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- PDB-9jx5: Solution NMR structure of the 1:1 complex of NOP56 intronic G-qua... -

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Basic information

Entry
Database: PDB / ID: 9jx5
TitleSolution NMR structure of the 1:1 complex of NOP56 intronic G-quadruplex bound with pyridostatin
ComponentsDNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3')
KeywordsDNA / antiparallel G4 / NOP56 oncogene / PDS
Function / homologyChem-7V8 / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYan, Z. / Wan, L. / Guo, P. / Han, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22004038 China
CitationJournal: Adv Sci / Year: 2025
Title: Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene.
Authors: Yan, Z. / He, A. / Wan, L. / Gao, Q. / Jiang, Y. / Wang, Y. / Wang, E. / Li, C. / Yang, Y. / Li, Y. / Guo, P. / Han, D.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 7, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1502
Polymers6,5531
Non-polymers5971
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6553.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-7V8 / 4-(2-azanylethoxy)-N2,N6-bis[4-(2-azanylethoxy)quinolin-2-yl]pyridine-2,6-dicarboxamide / Pyridostatin


Mass: 596.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H32N8O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN
Nonpolymer detailsN36+H33+H34+H35, N40+H30+H31+H32 and N52+H95+H96+H97 are three protonated (positive charged) amino ...N36+H33+H34+H35, N40+H30+H31+H32 and N52+H95+H96+H97 are three protonated (positive charged) amino groups. Therefore the valence of N36, N40 and N52 is four.

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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-1H TOCSY
141isotropic12D 1H-1H COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin, 99.96% D2O199.96% D2O
solution20.5 mM DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3'), 1 mM sodium phosphate, 0.02 mM DSS, 1.5 mM pyridostatin, 90% H2O/10% D2O290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3')natural abundance1
1 mMsodium phosphatenatural abundance1
0.02 mMDSSnatural abundance1
1.5 mMpyridostatinnatural abundance1
0.5 mMDNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3')natural abundance2
1 mMsodium phosphatenatural abundance2
0.02 mMDSSnatural abundance2
1.5 mMpyridostatinnatural abundance2
Sample conditionsIonic strength: 1 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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