4WYB

Structure of the Bud6 flank domain in complex with actin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2015.05.015
  • Primary Citation of Related Structures:  
    4WYB

  • 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 that binds monomeric actin ...

    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. Electronic address: eck@crystal.harvard.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
A,
C,
E,
G,
I,
K,
M,
O,
Q,
S,
U,
W [auth X]
377Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 6
B,
D,
F,
H,
J,
L,
N,
P,
R,
T,
V,
X [auth Y]
92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD6, AIP3, YLR319C, L8543.5
UniProt
Find proteins for P41697 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41697 
Go to UniProtKB:  P41697
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41697
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth E]
EA [auth G]
GA [auth I]
IA [auth K]
AA [auth C],
CA [auth E],
EA [auth G],
GA [auth I],
IA [auth K],
KA [auth M],
MA [auth O],
OA [auth Q],
QA [auth S],
SA [auth U],
UA [auth X],
Y [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth C]
DA [auth E]
FA [auth G]
HA [auth I]
JA [auth K]
BA [auth C],
DA [auth E],
FA [auth G],
HA [auth I],
JA [auth K],
LA [auth M],
NA [auth O],
PA [auth Q],
RA [auth S],
TA [auth U],
VA [auth X],
Z [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.753α = 90
b = 138.753β = 90
c = 356.651γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM071834
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM083137

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Data collection
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations