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- PDB-6tr2: Pre-folded structures govern folding pathways of human telomeric ... -

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Basic information

Entry
Database: PDB / ID: 6tr2
TitlePre-folded structures govern folding pathways of human telomeric G-quadruplexes
ComponentsDNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA / human telomere / G-quadruplex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, B. / Frelih, T. / Plavec, J. / Sket, P.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-7108 Slovenia
Slovenian Research AgencyJ3-7245 Slovenia
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Pre-folded structures govern folding pathways of human telomeric G-quadruplexes.
Authors: Frelih, T. / Wang, B. / Plavec, J. / Sket, P.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 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(*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,2881
Polymers7,2881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4320 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
121isotropic12D 1H-15N HSQC
131isotropic11D 1H-15N HSQC
142isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM 8% 13C, 8% 15N GCN, 90% H2O/10% D2OSite-specific 13C,15N labelled samples used for unambiguous assignment13C15N sample90% H2O/10% D2O
solution21 mM GCN, 90% H2O/10% D2Ounlabeled_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGCN8% 13C, 8% 15N1
1 mMGCNnatural abundance2
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Agilent Agilent Agilent Technologies DD2 600 MHz NMR spectrometer
Manufacturer: Agilent
Model: Agilent Agilent Technologies DD2 600 MHz NMR spectrometer
Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVarianprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
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 least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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