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- PDB-5mvb: Solution structure of a human G-Quadruplex hybrid-2 form in compl... -

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Basic information

Entry
Database: PDB / ID: 5mvb
TitleSolution structure of a human G-Quadruplex hybrid-2 form in complex with a Gold-ligand.
ComponentsDNA (26-MER)
KeywordsDNA / G-Quadruplex hybrid / 2 Auoxo6
Function / homologyChem-AUZ / : / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWirmer-Bartoschek, J. / Jonker, H.R.A. / Bendel, L.E. / Gruen, T. / Bazzicalupi, C. / Messori, L. / Gratteri, P. / Schwalbe, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
Land HessenLOEWE SynChemBio Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.
Authors: Wirmer-Bartoschek, J. / Bendel, L.E. / Jonker, H.R.A. / Grun, J.T. / Papi, F. / Bazzicalupi, C. / Messori, L. / Gratteri, P. / Schwalbe, H.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 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 1.4Jun 19, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0734
Polymers8,2001
Non-polymers8733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area4990 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (26-MER)


Mass: 8200.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-AUZ / bis(m2-Oxo)-bis(2-methyl-2,2'-bipyridine)-di-gold(iii)


Mass: 794.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24Au2N4O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D NOESY
222isotropic22D NOESY
131isotropic12D COSY
242isotropic12D COSY
252isotropic22D 1H-13C HSQC aliphatic
262isotropic2D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6, 93% H2O/ 7%DMSO-d6H2O93% H2O/ 7%DMSO-d6
solution21 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6, 93% D2O / 7% DMSO-d6D2O93% D2O / 7% DMSO-d6
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA 26mernatural abundance1
70 mMpotassium chloridenatural abundance1
25 mMKPinatural abundance1
0.3 mMDSSnatural abundance1
1.3 mMAuoxo6natural abundance1
1 mMDNA 26mernatural abundance2
70 mMpotassium chloridenatural abundance2
25 mMKPinatural abundance2
0.3 mMDSSnatural abundance2
1.3 mMAuoxo6natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
195 mMconditions_H2O7ambient mbar298 K
295 mMconditions_D2O7ambient mbar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001cryoprobe
Bruker AVANCEBrukerAVANCE7002cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
Sparky3.114Goddard and Knellerchemical shift assignment
Sparky3.114Goddard and Knellerpeak picking
Sparky3.114Goddard and Knellerdata analysis
ARIA1.2 HJ development versionLinge, O'Donoghue and Nilgesrefinement
ARIA1.2 HJ development versionLinge, O'Donoghue and Nilgesstructure calculation
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 6
Details: simulated annealing with cartesian angle dynamics; refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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