7D5E | pdb_00007d5e

Left-handed G-quadruplex containing two bulges

PDB DOI: https://doi.org/10.2210/pdb7D5E/pdb
NAKB: 7D5E

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.214 (Depositor), 0.229 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

Macromolecule Content

Total Structure Weight: 18.85 kDa
Atom Count: 1,450
Modeled Residue Count: 56
Deposited Residue Count: 56
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
2xBulge-LHG4motif	A, B	28	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], L [auth B], M [auth B]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.214 (Depositor), 0.229 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.185 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.1	α = 90
b = 39.81	β = 91.28
c = 54.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

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

Revision History (Full details and data files)

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