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PDBsum entry 1mdu
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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
1mdu

 

 

 

 

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Contents
Protein chains
124 a.a. *
361 a.a. *
Ligands
TRS
ATP ×2
Metals
_CA ×7
Waters ×471
* Residue conservation analysis
PDB id:
1mdu
Name: Structural protein
Title: Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1 (gs-1)
Structure: Gelsolin precursor. Chain: a, d. Fragment: actin-severing. Synonym: actin-depolymerizing factor, adf, brevin, agel. Engineered: yes. A-actin. Chain: b, e
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Gallus gallus. Chicken. Organism_taxid: 9031
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.193     R-free:   0.233
Authors: J.F.Dawson,E.P.Sablin,J.A.Spudich,R.J.Fletterick
Key ref:
J.F.Dawson et al. (2003). Structure of an F-actin trimer disrupted by gelsolin and implications for the mechanism of severing. J Biol Chem, 278, 1229-1238. PubMed id: 12356759 DOI: 10.1074/jbc.M209160200
Date:
07-Aug-02     Release date:   07-Jan-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		782 a.a.
124 a.a.
Protein chains
Pfam   ArchSchema ?
P68139  (ACTS_CHICK) -  Actin, alpha skeletal muscle from Gallus gallus
Seq:
Struc: 		377 a.a.
361 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains B, E: E.C.3.6.4.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1074/jbc.M209160200 J Biol Chem 278:1229-1238 (2003)
PubMed id: 12356759  
 
 
Structure of an F-actin trimer disrupted by gelsolin and implications for the mechanism of severing.
J.F.Dawson, E.P.Sablin, J.A.Spudich, R.J.Fletterick.
 
  ABSTRACT  
 
Stable oligomers of filamentous actin were obtained by cross-linking F-actin with 1,4-N,N'-phenylenedimaleimide and depolymerization with excess segment-1 of gelsolin. Segment-1-bound and cross-linked actin oligomers containing either two or three actin subunits were purified and shown to nucleate actin assembly. Kinetic assembly data from mixtures of monomeric actin and the actin oligomers fit a nucleation model where cross-linked actin dimer or trimer reacts with an actin monomer to produce a competent nucleus for filament assembly. We report the three-dimensional structure of the segment-1-actin hexamer containing three actin subunits, each with a tightly bound ATP. Comparative analysis of this structure with twelve other actin structures provides an atomic level explanation for the preferential binding of ATP by the segment-1-complexed actin. Although the structure of segment-1-bound actin trimer is topologically similar to the helical model of F-actin (1), it has a distorted symmetry compared with that of the helical model. This distortion results from intercalation of segment-1 between actin protomers that increase the rise per subunit and rotate each of the actin subunits relative to their positions in F-actin. We also show that segment-1 of gelsolin is able to sever actin filaments, although the severing activity of segment-1 is significantly lower than full-length gelsolin.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Structure of the GS-1-complexed actin trimer. Actin subunits in the trimer complex are colored in dark green, orange, and blue. The corresponding segments of gelsolin are light green, yellow, and cyan. The structure of each GS-1-bound protomer in the trimer is similar to the structures of GS-1-complexed actin solved previously. In each protomer, the bound nucleotide, Ca^2+-ATP, is shown as a gray space-filling model. Coordinated ions of Ca^2+ are drawn as red spheres. The pPDM cross-link is between Lys-193 of one actin subunit and Cys-376 of its neighbor. In each actin subunit, the C-terminal residues 375-377 and residues corresponding to DNase I binding loop are disordered and are not included in the model. The dashed lines, therefore, connect the cross-linked Lys-193 of subunits 1 and 2 to the last visible C-terminal residue, Arg-374, of subunits 2 and 3, respectively. 		Figure 6.
Fig. 6. Comparative analysis of the intersubunit contacts in the X-actin and F-actin filaments. A, structural elements forming the interface in the X-actin. Amino acid residues 197-199 (yellow), 225-238 (red), and 253-258 (orange) from an actin subunit N and residues 112-116 (light green), 174-180 (dark green), 271-274 (blue), and 285-289 (cyan) from an adjacent subunit N+1 are highlighted, and their positions are indicated in the F-actin filament (B). Magnified view of the structural elements buried at the X-actin interface (C) and their positions at the interface of the F-actin (D) are shown. Coloring scheme is consistent for all panels.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 1229-1238) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19767829 K.Pengelly, A.Loncar, A.A.Perieteanu, and J.F.Dawson (2009).
Cysteine engineering of actin self-assembly interfaces.
  Biochem Cell Biol, 87, 663-675.  
18391412 M.R.Sawaya, D.S.Kudryashov, I.Pashkov, H.Adisetiyo, E.Reisler, and T.O.Yeates (2008).
Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.
  Acta Crystallogr D Biol Crystallogr, 64, 454-465.
PDB codes: 2q1n 2q31 2q36
17167532 B.Sweeting, and J.F.Dawson (2006).
Purification and characterization of a nonpolymerizing long-pitch actin dimer.
  Biochem Cell Biol, 84, 695-702.  
16428279 T.J.Minehardt, P.A.Kollman, R.Cooke, and E.Pate (2006).
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin.
  Biophys J, 90, 2445-2449.  
16141336 D.S.Kudryashov, M.R.Sawaya, H.Adisetiyo, T.Norcross, G.Hegyi, E.Reisler, and T.O.Yeates (2005).
The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin.
  Proc Natl Acad Sci U S A, 102, 13105-13110.
PDB code: 2a5x
16192358 J.S.Allingham, A.Zampella, M.V.D'Auria, and I.Rayment (2005).
Structures of microfilament destabilizing toxins bound to actin provide insight into toxin design and activity.
  Proc Natl Acad Sci U S A, 102, 14527-14532.
PDB codes: 2asm 2aso 2asp
15060630 J.Summerscales, and J.F.Dawson (2004).
Probing Dictyostelium severin structure and function by cross linking to actin.
  Biochem Cell Biol, 82, 343-350.  
12923524 E.H.Egelman (2003).
A tale of two polymers: new insights into helical filaments.
  Nat Rev Mol Cell Biol, 4, 621-630.  
14578936 V.A.Klenchin, J.S.Allingham, R.King, J.Tanaka, G.Marriott, and I.Rayment (2003).
Trisoxazole macrolide toxins mimic the binding of actin-capping proteins to actin.
  Nat Struct Biol, 10, 1058-1063.
PDB codes: 1qz5 1qz6
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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