5VNT | pdb_00005vnt

Solution NMR Structure of the C-terminal Headpiece Domain of Villin 4 from A.thaliana, the First Non-Vertebrate Headpiece Structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Plant Villin Headpiece Domain Demonstrates a Novel Surface Charge Pattern and High Affinity for F-Actin.

Miears, H.L.Gruber, D.R.Horvath, N.M.Antos, J.M.Young, J.Sigurjonsson, J.P.Klem, M.L.Rosenkranz, E.A.Okon, M.McKnight, C.J.Vugmeyster, L.Smirnov, S.L.

(2018) Biochemistry 57: 1690-1701

  • DOI: https://doi.org/10.1021/acs.biochem.7b00856
  • Primary Citation Related Structures: 
    5VNT

  • PubMed Abstract: 

    Plants utilize multiple isoforms of villin, an F-actin regulating protein with an N-terminal gelsolin-like core and a distinct C-terminal headpiece domain. Unlike their vertebrate homologues, plant villins have a much longer linker polypeptide connecting the core and headpiece. Moreover, the linker-headpiece connection region in plant villins lacks sequence homology to the vertebrate villin sequences. It is unknown to what extent the plant villin headpiece structure and function resemble those of the well-studied vertebrate counterparts. Here we present the first solution NMR structure and backbone dynamics characterization of a headpiece from plants, villin isoform 4 from Arabidopsis thaliana. The villin 4 headpiece is a 63-residue domain (V4HP63) that adopts a typical headpiece fold with an aromatics core and a tryptophan-centered hydrophobic cap within its C-terminal subdomain. However, V4HP63 has a distinct N-terminal subdomain fold as well as a novel, high mobility loop due to the insertion of serine residue in the canonical sequence that follows the variable length loop in headpiece sequences. The domain binds actin filaments with micromolar affinity, like the vertebrate analogues. However, the V4HP63 surface charge pattern is novel and lacks certain features previously thought necessary for high-affinity F-actin binding. Utilizing the updated criteria for strong F-actin binding, we predict that the headpiece domains of all other villin isoforms in A. thaliana have high affinity for F-actin.


  • Organizational Affiliation
    • Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States.

Macromolecule Content 

  • Total Structure Weight: 7.5 kDa 
  • Atom Count: 528 
  • Modeled Residue Count: 63 
  • Deposited Residue Count: 63 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Villin-463Arabidopsis thalianaMutation(s): 0 
Gene Names: VLN4At4g30160F6G3.190F9N11.10
UniProt
Find proteins for O65570 (Arabidopsis thaliana)
Explore O65570 
Go to UniProtKB:  O65570
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO65570
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
WWUUnited StatesRSP Pilot Project

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references