1Y64

Bni1p Formin Homology 2 Domain complexed with ATP-actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain

Otomo, T.Tomchick, D.R.Otomo, C.Panchal, S.C.Machius, M.Rosen, M.K.

(2005) Nature 433: 488-494

  • DOI: 10.1038/nature03251

  • PubMed Abstract: 
  • The conserved formin homology 2 (FH2) domain nucleates actin filaments and remains bound to the barbed end of the growing filament. Here we report the crystal structure of the yeast Bni1p FH2 domain in complex with tetramethylrhodamine-actin. Each of ...

    The conserved formin homology 2 (FH2) domain nucleates actin filaments and remains bound to the barbed end of the growing filament. Here we report the crystal structure of the yeast Bni1p FH2 domain in complex with tetramethylrhodamine-actin. Each of the two structural units in the FH2 dimer binds two actins in an orientation similar to that in an actin filament, suggesting that this structure could function as a filament nucleus. Biochemical properties of heterodimeric FH2 mutants suggest that the wild-type protein equilibrates between two bound states at the barbed end: one permitting monomer binding and the other permitting monomer dissociation. Interconversion between these states allows processive barbed-end polymerization and depolymerization in the presence of bound FH2 domain. Kinetic and/or thermodynamic differences in the conformational and binding equilibria can explain the variable activity of different FH2 domains as well as the effects of the actin-binding protein profilin on FH2 function.


    Related Citations: 
    • The Core FH2 Domain of Diaphanous-Related Formins Is an Elongated Actin Binding Protein that Inhibits Polymerization
      Shimada, A.,Nyitrai, M.,Vetter, I.R.,Kuhlmann, D.,Bugyi, B.,Narumiya, S.,Geeves, M.A.,Wittinghofer, A.
      (2004) Mol.Cell 13: 511
    • Crystal Structures Of A Formin Homology-2 Domain Reveal A Tethered-Dimer Architecture
      Xu, Y.,Moseley, J.B.,Sagot, I.,Poy, F.,Pellman, D.,Goode, B.L.,Eck, M.J.
      (2004) Cell 116: 711


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
A
375Oryctolagus cuniculusGene Names: ACTA1 (ACTA)
Find proteins for P68135 (Oryctolagus cuniculus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68135
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BNI1 protein
B
443Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: BNI1 (PPF3, SHE5)
Find proteins for P41832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41832
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.289 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 231.997α = 90.00
b = 56.229β = 107.70
c = 100.945γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance