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PDBsum entry 2hmp

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
2hmp
Jmol
Contents
Protein chains
361 a.a.
Ligands
SPD
ATP ×2
EDO ×9
211 ×2
Metals
_SR ×7
Waters ×623
PDB id:
2hmp
Name: Structural protein
Title: Uncomplexed actin cleaved with protease ecp32
Structure: Actin, alpha skeletal muscle. Chain: a, b. Synonym: alpha-actin-1
Source: Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Organ: muscle
Resolution:
1.90Å     R-factor:   0.179     R-free:   0.215
Authors: V.A.Klenchin,S.Y.Khaitlina,I.Rayment
Key ref:
V.A.Klenchin et al. (2006). Crystal structure of polymerization-competent actin. J Mol Biol, 362, 140-150. PubMed id: 16893553 DOI: 10.1016/j.jmb.2006.07.001
Date:
11-Jul-06     Release date:   19-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68135  (ACTS_RABIT) -  Actin, alpha skeletal muscle
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)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     skeletal muscle fiber development   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2006.07.001 J Mol Biol 362:140-150 (2006)
PubMed id: 16893553  
 
 
Crystal structure of polymerization-competent actin.
V.A.Klenchin, S.Y.Khaitlina, I.Rayment.
 
  ABSTRACT  
 
All actin crystal structures reported to date represent actin complexed or chemically modified with molecules that prevent its polymerization. Actin cleaved with ECP32 protease at a single site between Gly42 and Val43 is virtually non-polymerizable in the Ca-ATP bound form but remains polymerization-competent in the Mg-bound form. Here, a crystal structure of the true uncomplexed ECP32-cleaved actin (ECP-actin) solved to 1.9 A resolution is reported. In contrast to the much more open conformation of the ECP-actin's nucleotide binding cleft in solution, the crystal structure of uncomplexed ECP-actin contains actin in a typical closed conformation similar to the complexed actin structures. This unambiguously demonstrates that the overall structure of monomeric actin is not significantly affected by a multitude of actin-binding proteins and toxins. The invariance of actin crystal structures suggests that the salt and precipitants necessary for crystallization stabilize actin in only one of its possible conformations. The asymmetric unit cell contains a new type of antiparallel actin dimer that may correspond to the "lower dimer" implicated in F-actin nucleation and branching. In addition, symmetry-related actin-actin contacts form a head to tail dimer that is strikingly similar to the longitudinal dimer predicted by the Holmes F-actin model, including a rotation of the monomers relative to each other not observed previously in actin crystal structures.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Actin cleavage by ECP32 protease. Shown is a ribbon diagram of a typical actin monomer and the location of a proteolytic cleavage site between Gly42 and Val43. The resulting two fragments (shown in cyan and magenta) remain associated such that the ECP-actin retains most of the features of the intact protein, including its ability to polymerize in the Mg-ATP bound form. Figure 1. Actin cleavage by ECP32 protease. Shown is a ribbon diagram of a typical actin monomer and the location of a proteolytic cleavage site between Gly42 and Val43. The resulting two fragments (shown in cyan and magenta) remain associated such that the ECP-actin retains most of the features of the intact protein, including its ability to polymerize in the Mg-ATP bound form.
Figure 6.
Figure 6. Molecular interface of the F-actin-like contacts in the ECP-actin crystal lattice. Residues comprising the molecular interface are shown as spacefill representations with carbon atoms colored as gray and orange for the different actin molecules. Oxygen atoms are red and nitrogen atoms are blue. Figure 6. Molecular interface of the F-actin-like contacts in the ECP-actin crystal lattice. Residues comprising the molecular interface are shown as spacefill representations with carbon atoms colored as gray and orange for the different actin molecules. Oxygen atoms are red and nitrogen atoms are blue.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 362, 140-150) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21585321 A.V.Morozova, S.Y.Khaitlina, and A.Y.Malinin (2011).
Heat Shock Protein DnaK - Substrate of Actin-Specific Bacterial Protease ECP32.
  Biochemistry (Mosc), 76, 455-461.  
21971041 D.N.Simon, and K.L.Wilson (2011).
The nucleoskeleton as a genome-associated dynamic 'network of networks'.
  Nat Rev Mol Cell Biol, 12, 695-708.  
20718862 A.V.Pivovarova, S.Y.Khaitlina, and D.I.Levitsky (2010).
Specific cleavage of the DNase-I binding loop dramatically decreases the thermal stability of actin.
  FEBS J, 277, 3812-3822.  
20946985 K.Murakami, T.Yasunaga, T.Q.Noguchi, Y.Gomibuchi, K.X.Ngo, T.Q.Uyeda, and T.Wakabayashi (2010).
Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
  Cell, 143, 275-287.
PDB codes: 3a5l 3a5m 3a5n 3a5o 3g37
20637412 T.Oda, and Y.Maéda (2010).
Multiple Conformations of F-actin.
  Structure, 18, 761-767.  
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.  
19710142 M.Harpen, T.Barik, A.Musiyenko, and S.Barik (2009).
Mutational analysis reveals a noncontractile but interactive role of actin and profilin in viral RNA-dependent RNA synthesis.
  J Virol, 83, 10869-10876.  
19935871 S.P.Yates, A.Loncar, and J.F.Dawson (2009).
Actin polymerization is controlled by residue size at position 204.
  Biochem Cell Biol, 87, 853-865.  
19158791 T.Oda, M.Iwasa, T.Aihara, Y.Maéda, and A.Narita (2009).
The nature of the globular- to fibrous-actin transition.
  Nature, 457, 441-445.
PDB code: 2zwh
19156817 T.Splettstoesser, F.Noé, T.Oda, and J.C.Smith (2009).
Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state.
  Proteins, 76, 353-364.  
18316411 I.Rouiller, X.P.Xu, K.J.Amann, C.Egile, S.Nickell, D.Nicastro, R.Li, T.D.Pollard, N.Volkmann, and D.Hanein (2008).
The structural basis of actin filament branching by the Arp2/3 complex.
  J Cell Biol, 180, 887-895.  
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
18938176 U.B.Nair, P.B.Joel, Q.Wan, S.Lowey, M.A.Rould, and K.M.Trybus (2008).
Crystal structures of monomeric actin bound to cytochalasin D.
  J Mol Biol, 384, 848-864.
PDB codes: 3eks 3eku 3el2
18022194 Y.Cong, M.Topf, A.Sali, P.Matsudaira, M.Dougherty, W.Chiu, and M.F.Schmid (2008).
Crystallographic conformers of actin in a biologically active bundle of filaments.
  J Mol Biol, 375, 331-336.
PDB codes: 3b5u 3b63
17873883 A.Orlova, E.C.Garner, V.E.Galkin, J.Heuser, R.D.Mullins, and E.H.Egelman (2007).
The structure of bacterial ParM filaments.
  Nat Struct Mol Biol, 14, 921-926.
PDB code: 2qu4
17612626 D.J.Teal, and J.F.Dawson (2007).
Yeast actin with a subdomain 4 mutation (A204C) exhibits increased pointed-end critical concentration.
  Biochem Cell Biol, 85, 319-325.  
17965017 E.Reisler, and E.H.Egelman (2007).
Actin structure and function: what we still do not understand.
  J Biol Chem, 282, 36133-36137.  
17351011 J.L.Melville, I.H.Moal, C.Baker-Glenn, P.E.Shaw, G.Pattenden, and J.D.Hirst (2007).
The structural determinants of macrolide-actin binding: in silico insights.
  Biophys J, 92, 3862-3867.  
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.