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crystal structure of Arabidopsis thaliana Profilin 2 complex with formin1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.922 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and computational examination of the Arabidopsis profilin-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. --: --

  • DOI: 10.1074/jbc.RA119.011307
  • Primary Citation of Related Structures:  

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

    Profilins are abundant cytosolic proteins that are universally expressed in eukaryotes and 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 poly-proline (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.


    Related Citations: 
    • Profilin 3 dynamictly regulate fomrin binding by its N terminal tail
      Qiao, Z.,Gao, Y.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Nanyang Technological University, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Profilin-2
B, A
131Arabidopsis thalianaMutation(s): 0 
Gene Names: PRO2 (PFN2, PRF2)
Find proteins for Q42418 (Arabidopsis thaliana)
Go to UniProtKB:  Q42418
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Formin-like protein 1
C, D
13Arabidopsis thalianaMutation(s): 0 
Gene Names: FH1 (AFH1)
Find proteins for Q9SE97 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SE97
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.922 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.523α = 90.00
b = 65.156β = 90.00
c = 73.533γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-08 
  • 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