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PDBsum entry 3b63

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protein Protein-protein interface(s) links
Contractile protein/structural protein PDB id
3b63
Jmol
Contents
Protein chains
365 a.a.
(+ 2 more) 364 a.a.
365 a.a.
PDB id:
3b63
Name: Contractile protein/structural protein
Title: Actin filament model in the extended form of acromsomal bund limulus sperm
Structure: Actin. Chain: a, g. Actin. Chain: b. Actin. Chain: c, i. Actin. Chain: d. Actin.
Source: Limulus polyphemus. Organism_taxid: 6850. Organism_taxid: 6850
Authors: Y.Cong,M.Topf,A.Sali,P.Matsudaira,M.Dougherty,W.Chiu,M.F.Sch
Key ref:
Y.Cong et al. (2008). Crystallographic conformers of actin in a biologically active bundle of filaments. J Mol Biol, 375, 331-336. PubMed id: 18022194 DOI: 10.1016/j.jmb.2007.10.027
Date:
26-Oct-07     Release date:   18-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P41340  (ACT3_LIMPO) -  Actin-3
Seq:
Struc:
376 a.a.
365 a.a.*
Protein chains
Pfam   ArchSchema ?
P41340  (ACT3_LIMPO) -  Actin-3
Seq:
Struc:
376 a.a.
364 a.a.*
Protein chains
Pfam   ArchSchema ?
P41340  (ACT3_LIMPO) -  Actin-3
Seq:
Struc:
376 a.a.
365 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 66 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biochemical function     nucleotide binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2007.10.027 J Mol Biol 375:331-336 (2008)
PubMed id: 18022194  
 
 
Crystallographic conformers of actin in a biologically active bundle of filaments.
Y.Cong, M.Topf, A.Sali, P.Matsudaira, M.Dougherty, W.Chiu, M.F.Schmid.
 
  ABSTRACT  
 
Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic understanding of actin function. The acrosomal bundle in the Limulus sperm has been shown to be a quasi-crystalline array with an asymmetric unit composed of a filament with 14 actin-scruin pairs. The bundle in its true discharge state penetrates the jelly coat of the egg. Our previous electron crystallographic reconstruction demonstrated that the actin filament cross-linked by scruin in this acrosomal bundle state deviates significantly from a perfect F-actin helix. In that study, the tertiary structure of each of the 14 actin protomers in the asymmetric unit of the bundle filament was assumed to be constant. In the current study, an actin filament atomic model in the acrosomal bundle has been refined by combining rigid-body docking with multiple actin crystal structures from the Protein Data Bank and constrained energy minimization. Our observation demonstrates that actin protomers adopt different tertiary conformations when they form an actin filament in the bundle. The scruin and bundle packing forces appear to influence the tertiary and quaternary conformations of actin in the filament of this biologically active bundle.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Actin crystal structure conformations and representation of 14 protomers in the asymmetric unit of the acrosomal actin bundle as a space-filling model. (a) Front view of several representative actin crystal structures illustrating the arrangement of the four actin subdomains and the difference in the secondary structures in subdomain 2, as discussed in the text (and encircled by a blue dashed line here). All the structures were aligned to subdomain 1 of 1ATN. The color scheme is as follows: 1ATN, red; 1HLU, gold; 1J6Z, green; 1YAG, ice blue; and 2BTF, pink. 1HLU (in gold) is obviously in a more open conformation compared with other structures. (b) C[α] representation of the asymmetric unit of the acrosomal bundle modeled with Holmes coordinates^5 after energy minimization in the context of the bundle. The actin subunits are shown in a slightly different color and shade. Each amino acid residue is represented by a sphere. Residues colored in red represent those whose C[α] moved by more than 2.5 Å from their original coordinates after energy minimization. (c) Protein Data Bank codes and positions of the nine structure coordinate sets (heterogeneous starting model) assigned to the 14 actins in the asymmetric unit. (d) C[α] of the heterogeneous starting model for the acrosomal filament after energy minimization.
Figure 3.
Fig. 3. Average density map of the 14 actin protomers in the acrosomal bundle asymmetric unit^4 along with the Holmes F-actin model (in cyan) and two representative x-ray structures of G-actin monomers (1MDU in light green and 1ESV in pink). Arrows indicate the hydrophobic loop that is extended toward the opposite strand in the Holmes structure and “parked” against its own monomer in the x-ray structures. Our average density is intermediate between these two extremes. (a) Top view, looking approximately down the filament axis. (b) Side view.
 
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 375, 331-336) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20687691 K.Amano, T.Yoshidome, M.Iwaki, M.Suzuki, and M.Kinoshita (2010).
Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models.
  J Chem Phys, 133, 045103.  
20222059 S.Grudinin, and S.Redon (2010).
Practical modeling of molecular systems with symmetries.
  J Comput Chem, 31, 1799-1814.  
19900461 Z.A.Oztug Durer, K.Diraviyam, D.Sept, D.S.Kudryashov, and E.Reisler (2010).
F-actin structure destabilization and DNase I binding loop: fluctuations mutational cross-linking and electron microscopy analysis of loop states and effects on F-actin.
  J Mol Biol, 395, 544-557.  
19234542 R.S.Gieni, and M.J.Hendzel (2009).
Actin dynamics and functions in the interphase nucleus: moving toward an understanding of nuclear polymeric actin.
  Biochem Cell Biol, 87, 283-306.  
19446530 Y.Cong, Q.Zhang, D.Woolford, T.Schweikardt, H.Khant, M.Dougherty, S.J.Ludtke, W.Chiu, and H.Decker (2009).
Structural mechanism of SDS-induced enzyme activity of scorpion hemocyanin revealed by electron cryomicroscopy.
  Structure, 17, 749-758.
PDB codes: 3ixv 3ixw
19015515 D.S.Kudryashov, Z.A.Durer, A.J.Ytterberg, M.R.Sawaya, I.Pashkov, K.Prochazkova, T.O.Yeates, R.R.Loo, J.A.Loo, K.J.Satchell, and E.Reisler (2008).
Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.
  Proc Natl Acad Sci U S A, 105, 18537-18542.
PDB codes: 3cjb 3cjc
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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