8Y2R | pdb_00008y2r

NMR Solution Structure of the 2:1 Coptisine-ATF4-G4 Complex

PDB DOI: https://doi.org/10.2210/pdb8Y2R/pdb
NAKB: 8Y2R

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

Deposited: 2024-01-27 Released: 2024-12-04
Deposition Author(s): Xiao, C.M., Li, Y.P., Liu, Y.S., Dong, R.F., He, X.Y., Lin, Q., Zang, X., Wang, K.B., Xia, Y.Z., Kong, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Overcoming Cancer Persister Cells by Stabilizing the ATF4 Promoter G-quadruplex.

Xiao, C., Li, Y., Liu, Y., Dong, R., He, X., Lin, Q., Zang, X., Wang, K., Xia, Y., Kong, L.

(2024) Adv Sci (Weinh) 11: e2401748-e2401748

PubMed: 38994891 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/advs.202401748
Primary Citation of Related Structures:
8Y2R

PubMed Abstract:
Persister cells (PS) selected for anticancer therapy have been recognized as a significant contributor to the development of treatment-resistant malignancies. It is found that imposing glutamine restriction induces the generation of PS, which paradoxically bestows heightened resistance to glutamine restriction treatment by activating the integrated stress response and initiating the general control nonderepressible 2-activating transcription factor 4-alanine, serine, cysteine-preferring transporter 2 (GCN2-ATF4-ASCT2) axis. Central to this phenomenon is the stress-induced ATF4 translational reprogramming. Unfortunately, directly targeting ATF4 protein has proven to be a formidable challenge because of its flat surface. Nonetheless, a G-quadruplex structure located within the promoter region of ATF4 (ATF4-G4) is uncovered and resolved, which functions as a transcriptional regulator and can be targeted by small molecules. The investigation identifies the natural compound coptisine (COP) as a potent binder that interacts with and stabilizes ATF4-G4. For the first time, the high-resolution structure of the COP-ATF4-G4 complex is determined. The formation of this stable complex disrupts the interaction between transcription factor AP-2 alpha (TFAP2A) and ATF4-G4, resulting in a substantial reduction in intracellular ATF4 levels and the eventual death of cancer cells. These seminal findings underscore the potential of targeting the ATF4-G4 structure to yield significant therapeutic advantages within the realm of persister cancer cells induced by glutamine-restricted therapy.

Organizational Affiliation

State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.

Macromolecule Content

Total Structure Weight: 7.66 kDa
Atom Count: 517
Modeled Residue Count: 22
Deposited Residue Count: 22
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPAPAPGPGPGPAPGPGPGPAPGPGPGPAPAPGPGPGPAPGPC(LIG)(LIG))-3')	A [auth X]	22	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KPT (Subject of Investigation/LOI) Query on KPT Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain B [auth X] MOL2 format, chain C [auth X] MOL2 format, chain B [auth X] mmCIF format, chain C [auth X] mmCIF format, chain B [auth X]	B [auth X], C [auth X]	6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium C₁₉ H₁₄ N O₄ XYHOBCMEDLZUMP-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain C [auth X]