4WYB

Structure of the Bud6 flank domain in complex with actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.493 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Bud6/Actin Complex Reveals a Novel WH2-like Actin Monomer Recruitment Motif.

Park, E.Graziano, B.R.Zheng, W.Garabedian, M.Goode, B.L.Eck, M.J.

(2015) Structure 23: 1492-1499

  • DOI: 10.1016/j.str.2015.05.015

  • PubMed Abstract: 
  • In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. The nucleation-enhancing activity of Bud6 requires both a "core" domain that binds to the formin and a "flank" domain ...

    In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. The nucleation-enhancing activity of Bud6 requires both a "core" domain that binds to the formin and a "flank" domain that binds monomeric actin. Here, we describe the structure of the Bud6 flank domain in complex with actin. Two helices in Bud6(flank) interact with actin; one binds in a groove at the barbed end of the actin monomer in a manner closely resembling the helix of WH2 domains, a motif found in many actin nucleation factors. The second helix rises along the face of actin. Mutational analysis verifies the importance of these Bud6-actin contacts for nucleation-enhancing activity. The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation.


    Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, SM1036, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
A, C, E, G, I, K, M, O, Q, S, U, X
377Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1 (ACTA)
Find proteins for P68135 (Oryctolagus cuniculus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68135
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bud site selection protein 6
B, D, F, H, J, L, N, P, R, T, V, Y
92Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BUD6 (AIP3)
Find proteins for P41697 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41697
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, X
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.493 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 138.753α = 90.00
b = 138.753β = 90.00
c = 356.651γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
Cootmodel building
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Data collection
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Refinement description