9MMF | pdb_00009mmf

First structure of Five-tetrad G-Quadruplex

• PDB DOI: https://doi.org/10.2210/pdb9MMF/pdb

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-12-20 Released: 2025-12-24 
• Deposition Author(s): Eyiolowope, J., Xing, E.R., Yatsunyk, L.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.236 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

The first crystal structure of five-tetrad G-quadruplex

Eyiolowope, J., Xing, E.R., Yatsunyk, L.A.

To be published.

Biological Assembly 1  

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

Biological Assembly Evidence: native gel electrophoresis, equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 10.04 kDa 
• Atom Count: 654 
• Modeled Residue Count: 31 
• Deposited Residue Count: 31 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (31-MER)	A	31	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A], C [auth A], D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.236 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.606	α = 90
b = 46.606	β = 90
c = 87.541	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Eyiolowope, J., Xing, E.R., Yatsunyk, L.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1R15CA253134

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release