7OAR

Crystal structure of helicase Pif1 from Thermus oshimai in complex with parallel G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.

Dai, Y.X.Guo, H.L.Liu, N.N.Chen, W.F.Ai, X.Li, H.H.Sun, B.Hou, X.M.Rety, S.Xi, X.G.

(2022) EMBO Rep 23: e53874-e53874

  • DOI: https://doi.org/10.15252/embr.202153874
  • Primary Citation of Related Structures:  
    7OAR

  • PubMed Abstract: 

    G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.


  • Organizational Affiliation

    College of Life Sciences, Northwest A&F University, Yangling, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pif1 helicase
A, B
450Thermus oshimaiMutation(s): 0 
UniProt
Find proteins for K7RJ88 (Thermus oshimai JL-2)
Explore K7RJ88 
Go to UniProtKB:  K7RJ88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7RJ88
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (28-MER)29Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF (Subject of Investigation/LOI)
Query on ALF

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
J [auth C],
K [auth C],
L [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.782α = 90
b = 151.782β = 90
c = 219.534γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870788, 11574252, 11774407
Centre National de la Recherche Scientifique (CNRS)FranceLIA Helicase-mediated GquadruplexDNA unwinding and genome stability

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-07-13
    Changes: Database references
  • Version 1.3: 2022-07-20
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description