6L3G

Structural Basis for DNA Unwinding at Forked dsDNA by two coordinating Pif1 helicases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for DNA unwinding at forked dsDNA by two coordinating Pif1 helicases.

Su, N.Byrd, A.K.Bharath, S.R.Yang, O.Jia, Y.Tang, X.Ha, T.Raney, K.D.Song, H.

(2019) Nat Commun 10: 5375-5375

  • DOI: https://doi.org/10.1038/s41467-019-13414-9
  • Primary Citation of Related Structures:  
    6L3G

  • PubMed Abstract: 

    Pif1 plays multiple roles in maintaining genome stability and preferentially unwinds forked dsDNA, but the mechanism by which Pif1 unwinds forked dsDNA remains elusive. Here we report the structure of Bacteroides sp Pif1 (BaPif1) in complex with a symmetrical double forked dsDNA. Two interacting BaPif1 molecules are bound to each fork of the partially unwound dsDNA, and interact with the 5' arm and 3' ss/dsDNA respectively. Each of the two BaPif1 molecules is an active helicase and their interaction may regulate their helicase activities. The binding of BaPif1 to the 5' arm causes a sharp bend in the 5' ss/dsDNA junction, consequently breaking the first base-pair. BaPif1 bound to the 3' ss/dsDNA junction impacts duplex unwinding by stabilizing the unpaired first base-pair and engaging the second base-pair poised for breaking. Our results provide an unprecedented insight into how two BaPif1 coordinate with each other to unwind the forked dsDNA.


  • Organizational Affiliation

    Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou, 310058, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent DNA helicaseB [auth A],
C [auth B]
433Bacteroides sp. AF32-8BHMutation(s): 0 
Gene Names: DWZ47_17845
UniProt
Find proteins for A0A373G551 (Bacteroides sp. AF32-8BH)
Explore A0A373G551 
Go to UniProtKB:  A0A373G551
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A373G551
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*TP*TP*TP*T)-3')A [auth D]30Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 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
Query on ALF

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG
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: 3.30 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.265α = 90
b = 131.265β = 90
c = 117.183γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XFITdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670820
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35GM122601

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description