8XGP | pdb_00008xgp

Solution NMR structure of an antiparallel chair-type G-quadruplex from NOP56 intron

• PDB DOI: https://doi.org/10.2210/pdb8XGP/pdb
• NAKB: 8XGP
• BMRB: 36625

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


• Deposited: 2023-12-15 Released: 2025-02-05 
• Deposition Author(s): Yan, Z., Guo, P., Han, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Insights into an Antiparallel Chair-Type G-Quadruplex From the Intron of NOP56 Oncogene.

Yan, Z., He, A., Wan, L., Gao, Q., Jiang, Y., Wang, Y., Wang, E., Li, C., Yang, Y., Li, Y., Guo, P., Han, D.

(2025) Adv Sci (Weinh) 12: e2406230-e2406230

• PubMed: 40047221 
• DOI: https://doi.org/10.1002/advs.202406230
• Primary Citation of Related Structures:  
  8XGP, 9JX5


• PubMed Abstract: 
  

  G-quadruplex (G4) structures play important roles in various biological processes, especially the gene regulation. Nucleolar protein 56 (NOP56) is an essential component in ribosome biogenesis while its overexpression associates with various types of cancers, rendering it a significant therapeutic target. Here for the first time, an antiparallel chair-type G4 structure formed by a 21-nt DNA sequence from the intron 1 of NOP56 is reported, and its high-resolution structure is determined using solution nuclear magnetic resonance spectroscopy. The NOP56-G4 has a special fold containing two G-tetrads and a C·G·C·G tetrad, which is further capped by a C∙C base pair. The G4 ligand pyridostatin (PDS) binds at the terminal G-tetrad through π-π stacking and electrostatic interactions, increasing the melting temperature of NOP56-G4 by ≈14 °C. This study further shows that PDS can significantly reduce NOP56 mRNA levels in three cancer cell lines. This work provides an unprecedented high-resolution structural basis for a special G4 structure from the intron of NOP56 and suggests a feasibility of targeting intronic G4 for gene regulation, propelling new avenues for G4 structure-based drug design and therapeutic strategy.

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Organizational Affiliation: 
• Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310013, China.
Zhejiang Laboratory, Hangzhou, Zhejiang, 311100, China.
College of Chemistry and Materials Science, Shanghai Normal University, Shanghai, 200234, China.
Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 6.55 kDa 
• Atom Count: 435 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*GP*CP*CP*TP*GP*GP*G)-3')	A	21	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Yan, Z., Guo, P., Han, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22004038

Revision History  

• Version 1.0: 2025-02-05
  Type: Initial release
  
• Version 1.1: 2025-03-19
  Changes: Database references
• Version 1.2: 2025-05-07
  Changes: Database references