5MVB | pdb_00005mvb

Solution structure of a human G-Quadruplex hybrid-2 form in complex with a Gold-ligand.

• PDB DOI: https://doi.org/10.2210/pdb5MVB/pdb
• NAKB: 5MVB
• BMRB: 34086

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-01-16 Released: 2017-05-31 
• Deposition Author(s): Wirmer-Bartoschek, J., Jonker, H.R.A., Bendel, L.E., Gruen, T., Bazzicalupi, C., Messori, L., Gratteri, P., Schwalbe, H.
• Funding Organization(s): Land Hessen

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding.

Wirmer-Bartoschek, J., Bendel, L.E., Jonker, H.R.A., Grun, J.T., Papi, F., Bazzicalupi, C., Messori, L., Gratteri, P., Schwalbe, H.

(2017) Angew Chem Int Ed Engl 56: 7102-7106

• PubMed: 28524432 
• DOI: https://doi.org/10.1002/anie.201702135
• Primary Citation Related Structures: 
  5MVB


• PubMed Abstract: 
  

  Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination.

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Organizational Affiliation: 
• Institute for Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60439, Frankfurt, Germany.
Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.
Dipartimento di Neuroscienze, Psicologia, Area del Farmaco, Salute del Bambino (NEUROFARBA), Università degli Studi di Firenze, via Ugo Schiff 6, 50019, Sesto Fiorentino, Italy.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 9.07 kDa 
• Atom Count: 579 
• Modeled Residue Count: 26 
• Deposited Residue Count: 26 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	A	26	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AUZ	D [auth A]	bis(m2-Oxo)-bis(2-methyl-2,2'-bipyridine)-di-gold(iii) C24 H24 Au2 N4 O2 GICNHPJNXLRXOX-UHFFFAOYSA-N
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Wirmer-Bartoschek, J., Jonker, H.R.A., Bendel, L.E., Gruen, T., Bazzicalupi, C., Messori, L., Gratteri, P., Schwalbe, H.

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Funding Organization	Location	Grant Number
Land Hessen	Germany	LOEWE SynChemBio

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Database references
• Version 1.2: 2018-01-17
  Changes: Structure summary
• Version 1.3: 2019-05-08
  Changes: Data collection
• Version 1.4: 2024-06-19
  Changes: Data collection, Database references, Derived calculations