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- PDB-5m1l: Structure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCG... -

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Basic information

Entry
Database: PDB / ID: 5m1l
TitleStructure of DNA AGCGA-quadruplex adopted by 15-mer d(GCGAGGGAGCGAGGG), VK34, oligonucleotide found in regulatory region of the PLEKHG3 human gene
ComponentsDNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')
KeywordsDNA / AGCGA-quadruplex / AGCGA-quadruplex family / GAGA-quartet / G-G N1-carbonyl symmetric base pair / PLEKHG3 gene
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKocman, V. / Plavec, J.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0242 Slovenia
Slovenian Research AgencyJ1-6733 Slovenia
CitationJournal: Nat Commun / Year: 2017
Title: Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions.
Authors: Kocman, V. / Plavec, J.
History
DepositionOct 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Data collection / Experimental preparation
Category: pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl_sample_conditions.pH / _pdbx_nmr_spectrometer.manufacturer
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*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')
B: DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)9,5302
Polymers9,5302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1440 Å2
ΔGint-17 kcal/mol
Surface area5090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / -
Representative

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Components

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


Mass: 4765.084 Da / Num. of mol.: 2 / 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
111isotropic22D 1H-1H NOESY
122isotropic11D 1H-15N HSQC
132isotropic12D 1H-15N HSQC
143isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2OVK3490% H2O/10% D2O
solution20.8 mM [10 % 15N] residue specific Gua DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2OVK3490% H2O/10% D2O
solution30.8 mM [10% 13C] residues specific adenine DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3'), 90% H2O/10% D2OVK3490% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')natural abundance1
0.8 mMDNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')[10 % 15N] residue specific Gua2
0.8 mMDNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*GP*AP*GP*GP*G)-3')[10% 13C] residues specific adenine3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System6001
Varian Uniform NMR SystemVarianUniform NMR System8002

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
NMR ensembleConformers submitted total number: 10

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