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- PDB-5o4d: G-quadruplex of Human papillomavirus type 52 -

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Basic information

Entry
Database: PDB / ID: 5o4d
TitleG-quadruplex of Human papillomavirus type 52
ComponentsDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / HPV52
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHuman papillomavirus type 52
MethodSOLUTION NMR / simulated annealing
AuthorsMarusic, M. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CitationJournal: Molecules / Year: 2019
Title: Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52.
Authors: Marusic, M. / Plavec, J.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
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*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,2771
Polymers7,2771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, structure runs as a monomer on native PAGE gel
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with lowest energy and least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 7276.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 52

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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
132isotropic12D 1H-1H TOCSY
142isotropic12D DQF-COSY
152isotropic22D HP COSY
163isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride, 90% H2O/10% D2ODNA was dissolved in solvent. Potassium phosphate and potassium chloride were added in steps to the final concentration.H2O sample90% H2O/10% D2O
solution21.2 mM DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride, 100% D2OH2O was exchanged to D2O in several steps of repeated lyophilization and dissolution in D2O.D2O sample100% D2O
solution30.9 mM 15N site-specifically labelled at 5% DNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3'), 10 mM potassium phosphate, 40 mM potassium chloride, 100% D2ODNA was dissolved in H2O. Potassium phosphate and potassium chloride were added in steps to the final concentration. H2O was exchanged to D2O in several steps of repeated lyophilization and dissolution in D2O.15N sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3')natural abundance1
10 mMpotassium phosphatenatural abundance1
40 mMpotassium chloridenatural abundance1
1.2 mMDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3')natural abundance2
10 mMpotassium phosphatenatural abundance2
40 mMpotassium chloridenatural abundance2
0.9 mMDNA (5'-D(*GP*GP*GP*TP*AP*GP*GP*GP*CP*AP*GP*GP*GP*GP*AP*CP*AP*CP*AP*GP*GP*GP*T)-3')15N site-specifically labelled at 5%3
10 mMpotassium phosphatenatural abundance3
40 mMpotassium chloridenatural abundance3
Sample conditionsIonic strength: 50 mM / Ionic strength err: 1 / Label: conditions_1 / pH: 6.8 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian DD2VarianDD26002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3Agilentcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.115Goddardpeak picking
Sparky3.115Goddarddata analysis
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Sparky3.115Goddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest energy and least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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