5Z8F | pdb_00005z8f

Solution structure for the unique dimeric 4:2 complex of a platinum(II)-based tripod bound to a hybrid-1 human telomeric G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb5Z8F/pdb
• BMRB: 36160
• NAKB: 5Z8F

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


• Deposited: 2018-01-31 Released: 2018-09-19 
• Deposition Author(s): Liu, W.T., Zhong, Y.F., Liu, L.Y., Zeng, W.J., Wang, F.Y., Yang, D.Z., Mao, Z.W.
• Funding Organization(s): 973 program, National Science Foundation of China, Ministry of Education of China, Science and Technology Planning Project of Guangdong Province

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structures of multiple G-quadruplex complexes induced by a platinum(II)-based tripod reveal dynamic binding

Liu, W., Zhong, Y.F., Liu, L.Y., Shen, C.T., Zeng, W., Wang, F., Yang, D., Mao, Z.W.

(2018) Nat Commun 9: 3496-3496

• PubMed: 30158518 
• DOI: https://doi.org/10.1038/s41467-018-05810-4
• Primary Citation Related Structures: 
  5Z80, 5Z8F


• PubMed Abstract: 
  

  DNA G-quadruplexes are not only attractive drug targets for cancer therapeutics, but also have important applications in supramolecular assembly. Here, we report a platinum(II)-based tripod (Pt-tripod) specifically binds the biological relevant hybrid-1 human telomeric G-quadruplex (Tel26), and strongly inhibits telomerase activity. Further investigations illustrate Pt-tripod induces the formation of monomeric and multimeric Pt-tripod‒Tel26 complex structures in solution. We solve the 1:1 and the unique dimeric 4:2 Pt-tripod-Tel26 complex structures by NMR. The structures indicate preferential binding of Pt-tripod to the 5'-end of Tel26 at a low Pt-tripod/Tel26 ratio of 0-1.0. After adding more Pt-tripod, the Pt-tripod binds the 3'-end of Tel26, unexpectedly inducing a unique dimeric 4:2 structure interlocked by an A:A non-canonical pair at the 3'-end. Our structures provide a structural basis for understanding the dynamic binding of small molecules with G-quadruplex and DNA damage mechanisms, and insights into the recognition and assembly of higher-order G-quadruplexes.

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Organizational Affiliation: 
• MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.
College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China.
Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University Center for Cancer Research, Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA. [e-mail].
MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China. [e-mail].
College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 21.96 kDa 
• Atom Count: 1,342 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9F0 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]-N,N-bis[4-[1-(2,5,8-triazonia-1$l^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]phenyl]aniline C45 H63 N13 Pt3 HWOQXVGDGHJZJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Liu, W.T., Zhong, Y.F., Liu, L.Y., Zeng, W.J., Wang, F.Y., Yang, D.Z., Mao, Z.W.

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Funding Organization	Location	Grant Number
973 program	China	2014CB845604 and 2015CB856301
National Science Foundation of China	China	21231007 and 21572282
Ministry of Education of China	China	IRT-17R111
Science and Technology Planning Project of Guangdong Province	China	2013B051000047 and 207999

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references