PDBsum entry: 1y64

Structural protein

PDB id: 1y64

Contents

Protein chains

357 a.a.

411 a.a. *

Ligands

ATP

Metals

_CA

* Residue conservation analysis

PDB id:

1y64

Name:

Structural protein

Title:

Bni1p formin homology 2 domain complexed with atp-actin

Structure:

Actin, alpha skeletal muscle. Chain: a. Synonym: alpha-actin 1. Bni1 protein. Chain: b. Fragment: fh2 domain, residues 1327-1769. Synonym: synthetic lethal 39. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: muscle. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: bni1, ppf3, she5. Expressed in: escherichia coli.

Resolution:

3.05Å R-factor: 0.289 R-free: 0.313

Authors:

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

Key ref:

T.Otomo et al. (2005). Structural basis of actin filament nucleation and processive capping by a formin homology 2 domain. Nature, 433, 488-494. PubMed id: 15635372 DOI: 10.1038/nature03251

Date:

03-Dec-04 Release date: 18-Jan-05

Protein chain

P68135  (ACTS_RABIT) -  Actin, alpha skeletal muscle

Seq: 377 a.a.

Struc: 357 a.a.*

Protein chain

P41832  (BNI1_YEAST) -  Protein BNI1

Seq: 1953 a.a.

Struc: 411 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (8 terms)
• Biological process: cellular component organization (12 terms)
• Biochemical function: nucleotide binding (6 terms)

DOI no: 10.1038/nature03251

Nature 433:488-494 (2005)

PubMed id: 15635372

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

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

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 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.

Selected figure(s)

Figure 1.
Figure 1: Structure of the FH2 -actin complex. a, Cartoon representation of packing in the TMR -actin -FH2 crystal. The asymmetric unit contains one FH2 monomer shown in either green or blue and one actin shown in pink or yellow. b, Stereo view of the structure of one bridge element of the FH2 domain (blue and green) in complex with two crystallographically related TMR -actins (pink and yellow). Figures were made with PyMol36. c, Three views of the structure of two bridge elements bound to three actins. Centre orientation is the same as in b. The FH2 monomers are shown as coloured cylinders and TMR -actins in surface representation. The linker between lasso and knob in the green FH2 monomer can be swapped with a crystallographically related lasso (dark blue), as indicated by the red arrow, to generate the ring-like topology of the FH2 dimer (right panel). The other linker in the blue FH2 monomer remains as in the crystal (left panel). Two bridges in the TMR -actin complex are located farther apart (103 Å, left panel) than in the structure of the free Bni1p FH2 dimer (80 Å)22.

Figure 5.
Figure 5: Model for FH2-mediated barbed end dynamics. Actin monomer is shown as a box with triangles and squares to indicate binding sites for the FH2 knob and post subdomains, respectively. FH2-bound sites are red, unbound sites are grey. The bridge element is shown as a bar with knob and post binding sites shaped to match the contact sites in actin. Bridges are blue and green, with black inter-bridge linkers. Actins are semi-transparent, to illustrate bridges and binding sites at the back of the structures. Actins held in the strained FH2-bound orientation are aligned with the page and light grey; actins in the filament orientation are tilted and dark grey. The configurational equilibrium between the closed and open states is determined by rate constants k[1] and k[-1]. The intermolecular binding equilibrium between the two states is determined by rate constants k[+] and k[-] and the concentration of actin monomer.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 433, 488-494) copyright 2005.

Figures were selected by the author.