7D5D | pdb_00007d5d

Left-handed G-quadruplex containing one bulge

• PDB DOI: https://doi.org/10.2210/pdb7D5D/pdb
• NAKB: 7D5D

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


• Deposited: 2020-09-25 Released: 2021-02-10 
• Deposition Author(s): Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.
• Funding Organization(s): National Research Foundation (NRF, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.168 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.119 (Depositor) 
• R-Value Observed: 
  0.121 (Depositor) 

Starting Model: experimental

Literature

Bulges in left-handed G-quadruplexes.

Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.

(2021) Nucleic Acids Res 49: 1724-1736

• PubMed: 33503265 
• DOI: https://doi.org/10.1093/nar/gkaa1259
• Primary Citation Related Structures: 
  7D5D, 7D5E, 7D5F


• PubMed Abstract: 
  

  G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.09 kDa 
• Atom Count: 786 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
1xBulge-LHG4motif	A	27	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	B [auth A], C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
K	D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.168 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.119 (Depositor) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.215	α = 90
b = 40.037	β = 115.87
c = 30.376	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Das, P., Ngo, K.H., Winnerdy, F.R., Maity, A., Bakalar, B., Mechulam, Y., Schmitt, E., Phan, A.T.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF-NRFI2017-09

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description