8IPP | pdb_00008ipp

Crystal structure of the complex between an ankyrin and a parallel G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb8IPP/pdb
• NAKB: 8IPP

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-14 Released: 2024-07-31 
• Deposition Author(s): Ngo, K.H., Liew, C.W., Heddi, B., Phan, A.T.
• Funding Organization(s): National Research Foundation (NRF, Singapore), Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.224 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.254 (DCC) 

Starting Models: experimental

Literature

Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein.

Ngo, K.H., Liew, C.W., Heddi, B., Phan, A.T.

(2024) J Am Chem Soc 146: 13709-13713

• PubMed: 38738955 
• DOI: https://doi.org/10.1021/jacs.4c01971
• Primary Citation Related Structures: 
  8IPF, 8IPP


• PubMed Abstract: 
  

  G-Quadruplex (G4) structures formed by guanine-rich DNA and RNA sequences are implicated in various biological processes. Understanding the mechanisms by which proteins recognize G4 structures is crucial for elucidating their functional roles. Here we present the X-ray crystal structure of an ankyrin protein bound to a parallel G4 structure. Our findings reveal a new specific recognition mode in which a bundle of α-helices and loops of the ankyrin form a flat surface to stack on the G-tetrad core. The protein employs a combination of hydrogen bonds and hydrophobic contacts to interact with the G4, and electrostatic interaction is used to enhance the binding affinity. This binding mechanism provides valuable insights into understanding G4 recognition by proteins.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore.
Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), UMR8113 CNRS, ENS Paris-Saclay, Gif-sur-Yvette 91190, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 20.16 kDa 
• Atom Count: 1,406 
• Modeled Residue Count: 142 
• Deposited Residue Count: 152 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin protein 2E4	B	136	synthetic construct	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
93del-T12	A	16	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.224 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.254 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.759	α = 90
b = 83.587	β = 90
c = 31.858	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: 2024-07-31 
Deposition Author(s): Ngo, K.H., Liew, C.W., Heddi, B., Phan, A.T.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF-NRFI2017-09
Ministry of Education (MoE, Singapore)	Singapore	MOE2018-T2-2-029

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release