6YJJ

Structure of CYRI-B (FAM49B) from Rhincodon typus (selenomethionine derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of CYRI-B (FAM49B), a key regulator of cellular actin assembly.

Kaplan, E.Stone, R.Hume, P.J.Greene, N.P.Koronakis, V.

(2020) Acta Crystallogr D Struct Biol 76: 1015-1024

  • DOI: 10.1107/S2059798320010906
  • Primary Citation of Related Structures:  
    6YJJ, 6YJK

  • PubMed Abstract: 
  • In eukaryotes, numerous fundamental processes are controlled by the WAVE regulatory complex (WRC) that regulates cellular actin polymerization, crucial for cell motility, cell-cell adhesion and epithelial differentiation. Actin assembly is triggered ...

    In eukaryotes, numerous fundamental processes are controlled by the WAVE regulatory complex (WRC) that regulates cellular actin polymerization, crucial for cell motility, cell-cell adhesion and epithelial differentiation. Actin assembly is triggered by interaction of the small GTPase Rac1 with CYFIP1, a key component of the WRC. Previously known as FAM49B, CYRI-B is a protein that is highly conserved across the Eukaryota and has recently been revealed to be a key regulator of Rac1 activity. Mutation of CYRI-B or alteration of its expression therefore leads to altered actin nucleation dynamics, with impacts on lamellipodia formation, cell migration and infection by intracellular pathogens. In addition, knockdown of CYRI-B expression in cancer cell lines results in accelerated cell proliferation and invasiveness. Here, the structure of Rhincodon typus (whale shark) CYRI-B is presented, which is the first to be reported of any CYRI family member. Solved by X-ray crystallography, the structure reveals that CYRI-B comprises three distinct α-helical subdomains and is highly structurally related to a conserved domain present in CYFIP proteins. The work presented here establishes a template towards a better understanding of CYRI-B biological function.


    Organizational Affiliation

    Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYRI-B (FAM49B)A325Rhincodon typusMutation(s): 0 
Gene Names: fam49b
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.4α = 90
b = 72.82β = 90
c = 107.32γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACrefinement
PHASERphasing
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-03 
  • Released Date: 2020-10-14 
  • Deposition Author(s): Kaplan, E.

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N000994/1
Wellcome TrustUnited Kingdom101828/Z/13/Z

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-10-21
    Changes: Database references