8D78 | pdb_00008d78

Crystal structure of a Ba stabilized four-tetrad, parallel Tetrahymena thermophila telomeric G-quadruplex in complex with N-methyl mesoporphyrin IX

• PDB DOI: https://doi.org/10.2210/pdb8D78/pdb
• NAKB: 8D78

• Classification: DNA
• Organism(s): Tetrahymena thermophila
• Mutation(s): No 


• Deposited: 2022-06-07 Released: 2023-07-05 
• Deposition Author(s): Chen, E.V., Beseiso, D., 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: 2.12 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Biophysical and structural characterization of telomeric G-quadruplexes from Tetrahymena thermophila in complex with N-Methyl Mesoporphyrin IX

Beseiso, D., Chen, E.V., Yatsunyk, L.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 7.9 kDa 
• Atom Count: 525 
• Modelled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3')	A	22	Tetrahymena thermophila

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMP	B [auth A]	N-METHYLMESOPORPHYRIN C35 H40 N4 O4 YNWHQWMCLCANDI-YIYRCNGCSA-N
BA	C [auth A], D [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.081	α = 90
b = 35.081	β = 90
c = 103.191	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Chen, E.V., Beseiso, D., 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: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description