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PDBsum entry 3ffk

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
3ffk
Jmol
Contents
Protein chains
347 a.a. *
365 a.a. *
Ligands
ATP ×2
Metals
_CA ×10
Waters ×473
* Residue conservation analysis
PDB id:
3ffk
Name: Structural protein
Title: Crystal structure of human gelsolin domains g1-g3 bound to a
Structure: Plasma gelsolin. Chain: a, d. Fragment: unp residues 52-426. Synonym: actin-depolymerizing factor. Adf. Brevin. Agel. Engineered: yes. Actin, alpha skeletal muscle. Chain: b, e. Synonym: alpha-actin-1
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gsn. Expressed in: escherichia coli. Expression_system_taxid: 562. Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986.
Resolution:
3.00Å     R-factor:   0.204     R-free:   0.273
Authors: S.Chumnarnsilpa,R.C.Robinson,L.D.Burtnick
Key ref:
S.Nag et al. (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. PubMed id: 19666512 DOI: 10.1073/pnas.0812374106
Date:
03-Dec-08     Release date:   06-Oct-09    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
347 a.a.
Protein chains
Pfam   ArchSchema ?
P68135  (ACTS_RABIT) -  Actin, alpha skeletal muscle
Seq:
Struc:
377 a.a.
365 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     skeletal muscle fiber development   2 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1073/pnas.0812374106 Proc Natl Acad Sci U S A 106:13713-13718 (2009)
PubMed id: 19666512  
 
 
Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin.
S.Nag, Q.Ma, H.Wang, S.Chumnarnsilpa, W.L.Lee, M.Larsson, B.Kannan, M.Hernandez-Valladares, L.D.Burtnick, R.C.Robinson.
 
  ABSTRACT  
 
Gelsolin consists of six homologous domains (G1-G6), each containing a conserved Ca-binding site. Occupation of a subset of these sites enables gelsolin to sever and cap actin filaments in a Ca-dependent manner. Here, we present the structures of Ca-free human gelsolin and of Ca-bound human G1-G3 in a complex with actin. These structures closely resemble those determined previously for equine gelsolin. However, the G2 Ca-binding site is occupied in the human G1-G3/actin structure, whereas it is vacant in the equine version. In-depth comparison of the Ca-free and Ca-activated, actin-bound human gelsolin structures suggests G2 and G6 to be cooperative in binding Ca(2+) and responsible for opening the G2-G6 latch to expose the F-actin-binding site on G2. Mutational analysis of the G2 and G6 Ca-binding sites demonstrates their interdependence in maintaining the compact structure in the absence of calcium. Examination of Ca binding by G2 in human G1-G3/actin reveals that the Ca(2+) locks the G2-G3 interface. Thermal denaturation studies of G2-G3 indicate that Ca binding stabilizes this fragment, driving it into the active conformation. The G2 Ca-binding site is mutated in gelsolin from familial amyloidosis (Finnish-type) patients. This disease initially proceeds through protease cleavage of G2, ultimately to produce a fragment that forms amyloid fibrils. The data presented here support a mechanism whereby the loss of Ca binding by G2 prolongs the lifetime of partially activated, intermediate conformations in which the protease cleavage site is exposed.
 
  Selected figure(s)  
 
Figure 1.
Structures of Ca-free human gelsolin and human G1–G3/actin. (A) Schematic representation of the structure of Ca-free human gelsolin. The arrowhead in this part, as in the others, points toward the peptide bond between Arg-172 and Ala-173, which gets cleaved in FAF. (B) The structure of human G1–G3 bound to actin. G2 is shown in a similar orientation as in A. There are five Ca^2+ ions (black spheres) associated with this structure, one bound to each gelsolin domain, another sandwiched between G1 and actin, and one at the ATP-binding site of actin. (C) Close up of the Ca-coordinating residues in G2 from human G1–G3/actin. Only G2–G3 is shown for clarity. (D) Close up of the vacant G2 Ca-binding site from equine G1–G3/actin (Protein Data Bank ID 1RGI). Protein representations were generated here and in the figures that follow by using PYMOL (http://pymol.sourceforge.net/).
Figure 2.
Structural interdependence of the G2 and G6 Ca-binding sites. (A) Schematic and electrostatic surface representations of Ca-free human gelsolin, highlighting the charged residues at the G2–G6 interface. (B) Schematic representations of Ca-bound G6 and G2, taken from the structures of Ca-bound equine G4–G6/actin (Protein Data Bank ID 1H1V) and human G1–G3/actin, respectively, in orientations similar to those presented in A. G2 and G6 have been translated relative to their positions in A to avoid steric clashes. Note that the Ca ions are coordinated by residues that previously made up the network of interactions between G2 and G6 in A.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264269 R.J.Perrin, R.Craig-Schapiro, J.P.Malone, A.R.Shah, P.Gilmore, A.E.Davis, C.M.Roe, E.R.Peskind, G.Li, D.R.Galasko, C.M.Clark, J.F.Quinn, J.A.Kaye, J.C.Morris, D.M.Holtzman, R.R.Townsend, and A.M.Fagan (2011).
Identification and validation of novel cerebrospinal fluid biomarkers for staging early Alzheimer's disease.
  PLoS One, 6, e16032.  
20140750 A.Van den Abbeele, S.De Clercq, A.De Ganck, V.De Corte, B.Van Loo, S.H.Soror, V.Srinivasan, J.Steyaert, J.Vandekerckhove, and J.Gettemans (2010).
A llama-derived gelsolin single-domain antibody blocks gelsolin-G-actin interaction.
  Cell Mol Life Sci, 67, 1519-1535.
PDB codes: 2x1o 2x1p 2x1q
20457765 P.Hotulainen, and C.C.Hoogenraad (2010).
Actin in dendritic spines: connecting dynamics to function.
  J Cell Biol, 189, 619-629.  
19904968 J.P.Solomon, I.T.Yonemoto, A.N.Murray, J.L.Price, E.T.Powers, W.E.Balch, and J.W.Kelly (2009).
The 8 and 5 kDa fragments of plasma gelsolin form amyloid fibrils by a nucleated polymerization mechanism, while the 68 kDa fragment is not amyloidogenic.
  Biochemistry, 48, 11370-11380.  
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.