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PDBsum entry 2fh3

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protein metals Protein-protein interface(s) links
Contractile protein PDB id
2fh3
Jmol
Contents
Protein chain
321 a.a. *
Metals
_CA ×9
Waters ×215
* Residue conservation analysis
PDB id:
2fh3
Name: Contractile protein
Title: C-terminal half of gelsolin soaked in low calcium at ph 8
Structure: Gelsolin. Chain: a, b, c. Fragment: c-terminal half domain. Synonym: actin-depolymerizing factor, adf, brevin, agel. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.87Å     R-factor:   0.203     R-free:   0.262
Authors: S.Chumnarnsilpa,A.Loonchanta,B.Xue,H.Choe,D.Urosev,H.Wang, L.D.Burtnick,R.C.Robinson
Key ref:
S.Chumnarnsilpa et al. (2006). Calcium ion exchange in crystalline gelsolin. J Mol Biol, 357, 773-782. PubMed id: 16466744 DOI: 10.1016/j.jmb.2006.01.026
Date:
23-Dec-05     Release date:   13-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
321 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     actin binding     1 term  

 

 
DOI no: 10.1016/j.jmb.2006.01.026 J Mol Biol 357:773-782 (2006)
PubMed id: 16466744  
 
 
Calcium ion exchange in crystalline gelsolin.
S.Chumnarnsilpa, A.Loonchanta, B.Xue, H.Choe, D.Urosev, H.Wang, U.Lindberg, L.D.Burtnick, R.C.Robinson.
 
  ABSTRACT  
 
Gelsolin is a calcium and pH-sensitive modulator of actin filament length. Here, we use X-ray crystallography to examine the extraction and exchange of calcium ions from their binding sites in different crystalline forms of the activated N and C-terminal halves of gelsolin, G1-G3 and G4-G6, respectively. We demonstrate that the combination of calcium and low pH activating conditions do not induce conformational changes in G4-G6 beyond those elicited by calcium alone. EGTA is able to remove calcium ions bound to the type I and type II metal ion-binding sites in G4-G6. Constrained by crystal contacts and stabilized by interdomain interaction surfaces, the gross structure of calcium-depleted G4-G6 remains that of the activated form. However, high-resolution details of changes in the ion-binding sites may represent the initial steps toward restoration of the arrangement of domains found in the calcium-free inactive form of gelsolin in solution. Furthermore, bathing crystals with the trivalent calcium ion mimic, Tb(3+), results in anomalous scattering data that permit unequivocal localization of terbium ions in each of the proposed type I and type II ion-binding sites of both halves of gelsolin. In contrast to predictions based on solution studies, we find that no calcium ion is immune to exchange.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The structure of G4-G6 at pH 4.5. (a) A stereo cartoon representation of the high-resolution structure of G4-G6 subjected to the initial wash conditions at pH 4.5. The domains are coloured: G4, pink; G5, green; and G6, orange. The terbium anomalous electron density map, contoured at 5 s (cyan), is superimposed onto the structure. Three terbium ion positions, characterized by the positive density in this map, are identical with the positions of type II calcium ions in this high-resolution structure and are labeled G4:II, G5:II and G6:II. The fourth terbium ion (G4:I) is in a position where calcium is not found in the high-resolution structure, but is found in the G4-G6:actin structure.15 (b) A cartoon representation of G4-G6 taken from the calcium-free form of gelsolin (PDB i.d. 1D0N),6 for purposes of comparison. In this state, the core b-sheet of G4 (pink) abuts that of G6 (orange), constituting the G4-G6 latch.15
Figure 7.
Figure 7. Terbium ion substitution in G1-G3. (a) A cartoon representation of the structure of G1-G3/actin (PDB i.d. 1RGI). Actin is coloured blue and the domains of gelsolin are coloured: G1, red; G2, light green; and G3, yellow. The P3[1]21 terbium anomalous difference electron density map, contoured at 5 s (black) and derived from terbium-soaked crystals of G1-G3/actin, is superimposed onto the structure. Three terbium ion positions, characterized by the positive density in this map, are identical with the positions of type II metal ion-binding sites in the G1-G3/actin structure and are labeled G1:II, G2:II and G3:II. A fourth terbium ion (G1:I) is in a position where a type I calcium ion is found in the structure.5 An actin-ATP-associated Tb^3+ (labelled A) also is indicated. (b) A cartoon representation of the structure of G1-G3/actin, with a P6[5]22 Tb^3+ anomalous electron density map superimposed, as in (a). In this case, the terbium ion-soaked crystals were backwashed with mother liquor containing 10 mM CaCl[2] and 0.2 mM Tb(NO[3])[3]. Tb^3+ was replaced only at the type II sites in G1 and G3. The type II site in G2, which was unoccupied in the structure of G1-G3/actin, and the type I site sandwiched between actin and G1 remained occupied by terbium ions.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 773-782) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19666512 S.Nag, Q.Ma, H.Wang, S.Chumnarnsilpa, W.L.Lee, M.Larsson, B.Kannan, M.Hernandez-Valladares, L.D.Burtnick, and R.C.Robinson (2009).
Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin.
  Proc Natl Acad Sci U S A, 106, 13713-13718.
PDB codes: 3ffk 3ffn
17604278 Ashish, M.S.Paine, P.B.Perryman, L.Yang, H.L.Yin, and J.K.Krueger (2007).
Global structure changes associated with Ca2+ activation of full-length human plasma gelsolin.
  J Biol Chem, 282, 25884-25892.  
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