6IQF

crystal structure of Arabidopsis thaliana Profilin 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and computational examination of theArabidopsisprofilin-Poly-P complex reveals mechanistic details in profilin-regulated actin assembly.

Qiao, Z.Sun, H.Ng, J.T.Y.Ma, Q.Koh, S.H.Mu, Y.Miao, Y.Gao, Y.G.

(2019) J Biol Chem 294: 18650-18661

  • DOI: 10.1074/jbc.RA119.011307
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Profilins are abundant cytosolic proteins that are universally expressed in eukaryotes and that regulate actin filament elongation by binding to both monomeric actin (G-actin) and formin proteins. The atypical profilin Arabidopsis AtPRF3 has ...

    Profilins are abundant cytosolic proteins that are universally expressed in eukaryotes and that regulate actin filament elongation by binding to both monomeric actin (G-actin) and formin proteins. The atypical profilin Arabidopsis AtPRF3 has been reported to cooperate with canonical profilin isoforms in suppressing formin-mediated actin polymerization during plant innate immunity responses. AtPRF3 has a 37-amino acid-long N-terminal extension (NTE), and its suppressive effect on actin assembly is derived from enhanced interaction with the polyproline (Poly-P) of the formin AtFH1. However, the molecular mechanism remains unclear. Here, we solved the crystal structures of AtPRF3Δ22 and AtPRF3Δ37, as well as AtPRF2 apo form and in complex with AtFH1 Poly-P at 1.5-3.6 Å resolutions. By combining these structures with molecular modeling, we found that AtPRF3Δ22 NTE has high plasticity, with a primary "closed" conformation that can adopt an open conformation that enables Poly-P binding. Furthermore, using molecular dynamics simulation and free-energy calculations of protein-protein binding, along with experimental validation, we show that the AtPRF3Δ22 binds to Poly-P in an adaptive manner, thereby enabling different binding modes that maintain the interaction through disordered sequences. Together, our structural and simulation results suggest that the dynamic conformational changes of the AtPRF3 NTE upon Poly-P binding modulate their interactions to fine-tune formin-mediated actin assembly.


    Organizational Affiliation

    Nanyang Technological University Institute of Structural Biology, Nanyang Technological University, 639798 Singapore.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRF3
A
131Arabidopsis thalianaMutation(s): 0 
Gene Names: PRF3PRO5At5g56600MIK19.4
Find proteins for Q9FE63 (Arabidopsis thaliana)
Go to UniProtKB:  Q9FE63
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.987α = 90
b = 52.862β = 110.38
c = 32.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-07 
  • Released Date: 2019-11-06 
  • Deposition Author(s): Qiao, Z., Gao, Y.

Funding OrganizationLocationGrant Number
Singapore--

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references