6IQK

crystal structure of Arabidopsis thaliana Profilin 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.313 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1074/jbc.RA119.011307
  • Primary Citation of Related Structures:  
    6IQF, 6IQI, 6IQJ, 6IQK

  • 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 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

    School of Biological Sciences, Nanyang Technological University, 637551 Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Profilin-5140Arabidopsis thalianaMutation(s): 0 
Gene Names: PRO5PRF3At5g56600MIK19.4
UniProt
Find proteins for Q9FE63 (Arabidopsis thaliana)
Explore Q9FE63 
Go to UniProtKB:  Q9FE63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FE63
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AtPRF3264Arabidopsis thalianaMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.313 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.9α = 90
b = 153.37β = 90
c = 196.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references