4DIX

Crystal structure of the Ig-PH domain of actin-binding protein SCAB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Plant actin-binding protein SCAB1 is dimeric actin cross-linker with atypical pleckstrin homology domain

Zhang, W.Zhao, Y.Guo, Y.Ye, K.

(2012) J Biol Chem 287: 11981-11990

  • DOI: 10.1074/jbc.M111.338525
  • Primary Citation of Related Structures:  
    4DIX, 4DJG

  • PubMed Abstract: 
  • SCAB1 is a novel plant-specific actin-binding protein that binds, bundles, and stabilizes actin filaments and regulates stomatal movement. Here, we dissected the structure and function of SCAB1 by structural and biochemical approaches. We show that SCAB1 is composed of an actin-binding domain, two coiled-coil (CC) domains, and a fused immunoglobulin and pleckstrin homology (Ig-PH) domain ...

    SCAB1 is a novel plant-specific actin-binding protein that binds, bundles, and stabilizes actin filaments and regulates stomatal movement. Here, we dissected the structure and function of SCAB1 by structural and biochemical approaches. We show that SCAB1 is composed of an actin-binding domain, two coiled-coil (CC) domains, and a fused immunoglobulin and pleckstrin homology (Ig-PH) domain. We determined crystal structures for the CC1 and Ig-PH domains at 1.9 and 1.7 Å resolution, respectively. The CC1 domain adopts an antiparallel helical hairpin that further dimerizes into a four-helix bundle. The CC2 domain also mediates dimerization. At least one of the coiled coils is required for actin binding, indicating that SCAB1 is a bivalent actin cross-linker. The key residues required for actin binding were identified. The PH domain lacks a canonical basic phosphoinositide-binding pocket but can bind weakly to inositol phosphates via a basic surface patch, implying the involvement of inositol signaling in SCAB1 regulation. Our results provide novel insights into the functional organization of SCAB1.


    Organizational Affiliation

    College of Biological Sciences, China Agricultural University, Beijing 10019, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plectin-related proteinA, B230Arabidopsis thalianaMutation(s): 0 
Gene Names: At2g26770SCAB1F18A8.14
UniProt
Find proteins for O48791 (Arabidopsis thaliana)
Explore O48791 
Go to UniProtKB:  O48791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48791
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.329α = 90
b = 76.329β = 90
c = 161.856γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2012-02-01 
  • Released Date: 2012-02-29 
  • Deposition Author(s): Zhang, W., Ye, K.

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references