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PDBsum entry 1izn

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protein ligands Protein-protein interface(s) links
Protein binding PDB id
1izn
Jmol
Contents
Protein chains
275 a.a. *
270 a.a. *
Ligands
NO3 ×4
Waters ×513
* Residue conservation analysis
PDB id:
1izn
Name: Protein binding
Title: Crystal structure of actin filament capping protein capz
Structure: Capz alpha-1 subunit. Chain: a, c. Synonym: f-actin capping protein alpha-1 subunit. Engineered: yes. Capz beta-1 subunit. Chain: b, d. Synonym: f-actin capping protein beta subunit isoform 1. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the cdnas encoding alpha-1 and beta-1 subunits were cloned in a single vector
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.222     R-free:   0.262
Authors: A.Yamashita,K.Maeda,Y.Maeda
Key ref:
A.Yamashita et al. (2003). Crystal structure of CapZ: structural basis for actin filament barbed end capping. EMBO J, 22, 1529-1538. PubMed id: 12660160 DOI: 10.1093/emboj/cdg167
Date:
10-Oct-02     Release date:   08-Apr-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13127  (CAZA1_CHICK) -  F-actin-capping protein subunit alpha-1
Seq:
Struc:
286 a.a.
275 a.a.
Protein chains
Pfam   ArchSchema ?
P14315  (CAPZB_CHICK) -  F-actin-capping protein subunit beta isoforms 1 and 2
Seq:
Struc:
277 a.a.
270 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     WASH complex   15 terms 
  Biological process     regulation of protein kinase C signaling cascade   14 terms 
  Biochemical function     actin binding     3 terms  

 

 
DOI no: 10.1093/emboj/cdg167 EMBO J 22:1529-1538 (2003)
PubMed id: 12660160  
 
 
Crystal structure of CapZ: structural basis for actin filament barbed end capping.
A.Yamashita, K.Maeda, Y.Maéda.
 
  ABSTRACT  
 
Capping protein, a heterodimeric protein composed of alpha and beta subunits, is a key cellular component regulating actin filament assembly and organization. It binds to the barbed ends of the filaments and works as a 'cap' by preventing the addition and loss of actin monomers at the end. Here we describe the crystal structure of the chicken sarcomeric capping protein CapZ at 2.1 A resolution. The structure shows a striking resemblance between the alpha and beta subunits, so that the entire molecule has a pseudo 2-fold rotational symmetry. CapZ has a pair of mobile extensions for actin binding, one of which also provides concomitant binding to another protein for the actin filament targeting. The mobile extensions probably form flexible links to the end of the actin filament with a pseudo 2(1) helical symmetry, enabling the docking of the two in a symmetry mismatch.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Actin-binding extensions of CapZ. (A) The regions crucial for actin binding [residues 259-C-terminus( ) and 266-C-terminus( )], the segment which exhibits actin-binding ability [residues 253-C-terminus( )] and the regions that are not required for high-affinity actin binding [residues N-terminus-115( ) and N-terminus-86( )] are mapped in red, orange and gray, respectively, on the CapZ structure based on the previous deletion mutant experiments (Hug et al., 1992; Casella and Torres, 1994; Sizonenko et al., 1996). The two conserved arginine residues, Arg259( ) and Arg244( ), are indicated with ball-and-stick models. (B) Surface representations of the C-terminal extension (residues 246 -271, the sole variant region between the isoforms) of two isoforms of , 1 (the present structure) and 2 (a homology model). The left two panels show the hydrophobic sides of the helices, and the right two panels show the hydrophilic sides. Hydrophobic, acidic and basic residues are colored in yellow, red and blue, respectively. Possible actin-binding sites are highlighted with red circles. (C) Surface representations of helix 6 (residues 270 -276) of the subunit. The color coding is the same as in (B).
Figure 4.
Figure 4 Actin -CapZ interaction. (A) Surface representations of an actin filament model (Lorenz et al., 1993), viewed from two different directions. In the left panel, the filament axis runs across and oblique to the plane of the page with the barbed end in the foreground, while in the right panel, the axis runs on the plane. The cones at the sides of the filaments indicate the filament orientations with the apex and the base indicating the pointed and barbed ends, respectively. One of the two actin molecules at the barbed end is colored in pink, and the hydrophobic residues on its surface are in yellow. The hydrophobic patches are highlighted with circles. The other actin molecule at the end is colored in cyan. The molecular surface of CapZ is also shown on the same scale, with the pair of C-terminal extensions [residues (260-C-terminus) and (245-C-terminus)] in red, and the N-terminal domains (residues (N-terminus-115) and (N-terminus-86)] in gray. (B) Schematic drawings of the possible binding modes of capping protein to the actin filament (speculative models).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 1529-1538) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21378753 A.Narita, T.Oda, and Y.Maéda (2011).
Structural basis for the slow dynamics of the actin filament pointed end.
  EMBO J, 30, 1230-1237.
PDB code: 2y83
20154706 A.R.Cole, L.P.Lewis, and H.Walden (2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
  Nat Struct Mol Biol, 17, 294-298.
PDB code: 3k1l
20188736 B.Russell, M.W.Curtis, Y.E.Koshman, and A.M.Samarel (2010).
Mechanical stress-induced sarcomere assembly for cardiac muscle growth in length and width.
  J Mol Cell Cardiol, 48, 817-823.  
20357771 M.Hernandez-Valladares, T.Kim, B.Kannan, A.Tung, A.H.Aguda, M.Larsson, J.A.Cooper, and R.C.Robinson (2010).
Structural characterization of a capping protein interaction motif defines a family of actin filament regulators.
  Nat Struct Mol Biol, 17, 497-503.  
20532239 M.Hertzog, F.Milanesi, L.Hazelwood, A.Disanza, H.Liu, E.Perlade, M.G.Malabarba, S.Pasqualato, A.Maiolica, S.Confalonieri, C.Le Clainche, N.Offenhauser, J.Block, K.Rottner, P.P.Di Fiore, M.F.Carlier, N.Volkmann, D.Hanein, and G.Scita (2010).
Molecular basis for the dual function of Eps8 on actin dynamics: bundling and capping.
  PLoS Biol, 8, e1000387.  
20075609 N.Watanabe (2010).
Inside view of cell locomotion through single-molecule: fast F-/G-actin cycle and G-actin regulation of polymer restoration.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 62-83.  
20625546 S.Takeda, S.Minakata, R.Koike, I.Kawahata, A.Narita, M.Kitazawa, M.Ota, T.Yamakuni, Y.Maéda, and Y.Nitanai (2010).
Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition.
  PLoS Biol, 8, e1000416.
PDB codes: 3aa0 3aa1 3aa6 3aa7 3aaa
20637412 T.Oda, and Y.Maéda (2010).
Multiple Conformations of F-actin.
  Structure, 18, 761-767.  
19682250 M.Ganter, H.Schüler, and K.Matuschewski (2009).
Vital role for the Plasmodium actin capping protein (CP) beta-subunit in motility of malaria sporozoites.
  Mol Microbiol, 74, 1356-1367.  
19830582 P.K.Luther (2009).
The vertebrate muscle Z-disc: sarcomere anchor for structure and signalling.
  J Muscle Res Cell Motil, 30, 171-185.  
19295171 T.J.Hartman, J.L.Martin, R.J.Solaro, A.M.Samarel, and B.Russell (2009).
CapZ dynamics are altered by endothelin-1 and phenylephrine via PIP2- and PKC-dependent mechanisms.
  Am J Physiol Cell Physiol, 296, C1034-C1039.  
18272787 C.T.Pappas, N.Bhattacharya, J.A.Cooper, and C.C.Gregorio (2008).
Nebulin interacts with CapZ and regulates thin filament architecture within the Z-disc.
  Mol Biol Cell, 19, 1837-1847.  
17855399 H.Cheng, B.H.Kim, and N.V.Grishin (2008).
MALISAM: a database of structurally analogous motifs in proteins.
  Nucleic Acids Res, 36, D211-D217.  
18544499 J.A.Cooper, and D.Sept (2008).
New insights into mechanism and regulation of actin capping protein.
  Int Rev Cell Mol Biol, 267, 183-206.  
17569543 B.Wawro, N.J.Greenfield, M.A.Wear, J.A.Cooper, H.N.Higgs, and S.E.Hitchcock-DeGregori (2007).
Tropomyosin regulates elongation by formin at the fast-growing end of the actin filament.
  Biochemistry, 46, 8146-8155.  
17656356 J.R.Kuhn, and T.D.Pollard (2007).
Single molecule kinetic analysis of actin filament capping. Polyphosphoinositides do not dissociate capping proteins.
  J Biol Chem, 282, 28014-28024.  
17182619 K.Kim, M.E.McCully, N.Bhattacharya, B.Butler, D.Sept, and J.A.Cooper (2007).
Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein: implications for how capping protein binds the actin filament.
  J Biol Chem, 282, 5871-5879.  
17470424 T.M.Wishart, J.M.Paterson, D.M.Short, S.Meredith, K.A.Robertson, C.Sutherland, M.A.Cousin, M.B.Dutia, T.H.Gillingwater, T.M.Wishart, J.M.Paterson, D.M.Short, S.Meredith, K.A.Robertson, C.Sutherland, M.A.Cousin, M.B.Dutia, and T.H.Gillingwater (2007).
Differential proteomics analysis of synaptic proteins identifies potential cellular targets and protein mediators of synaptic neuroprotection conferred by the slow Wallerian degeneration (Wlds) gene.
  Mol Cell Proteomics, 6, 1318-1330.  
17360616 V.O.Paavilainen, M.Hellman, E.Helfer, M.Bovellan, A.Annila, M.F.Carlier, P.Permi, and P.Lappalainen (2007).
Structural basis and evolutionary origin of actin filament capping by twinfilin.
  Proc Natl Acad Sci U S A, 104, 3113-3118.
PDB code: 2hd7
17110933 A.Narita, S.Takeda, A.Yamashita, and Y.Maéda (2006).
Structural basis of actin filament capping at the barbed-end: a cryo-electron microscopy study.
  EMBO J, 25, 5626-5633.  
  16569237 D.L.Scott, G.Diez, and W.H.Goldmann (2006).
Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data.
  Theor Biol Med Model, 3, 17.  
16959963 J.B.Moseley, and B.L.Goode (2006).
The yeast actin cytoskeleton: from cellular function to biochemical mechanism.
  Microbiol Mol Biol Rev, 70, 605-645.  
  16914033 J.Smith, G.Diez, A.H.Klemm, V.Schewkunow, and W.H.Goldmann (2006).
CapZ-lipid membrane interactions: a computer analysis.
  Theor Biol Med Model, 3, 30.  
16565070 K.L.Damm, and H.A.Carlson (2006).
Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures.
  Biophys J, 90, 4558-4573.  
16866873 K.Nakano, and I.Mabuchi (2006).
Actin-capping protein is involved in controlling organization of actin cytoskeleton together with ADF/cofilin, profilin and F-actin crosslinking proteins in fission yeast.
  Genes Cells, 11, 893-905.  
16895918 N.Bhattacharya, S.Ghosh, D.Sept, and J.A.Cooper (2006).
Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end.
  J Biol Chem, 281, 31021-31030.  
16436516 S.Huang, L.Gao, L.Blanchoin, and C.J.Staiger (2006).
Heterodimeric capping protein from Arabidopsis is regulated by phosphatidic acid.
  Mol Biol Cell, 17, 1946-1958.  
16434392 T.Uruno, K.Remmert, and J.A.Hammer (2006).
CARMIL is a potent capping protein antagonist: identification of a conserved CARMIL domain that inhibits the activity of capping protein and uncaps capped actin filaments.
  J Biol Chem, 281, 10635-10650.  
15831458 D.A.Canton, M.E.Olsten, K.Kim, A.Doherty-Kirby, G.Lajoie, J.A.Cooper, and D.W.Litchfield (2005).
The pleckstrin homology domain-containing protein CKIP-1 is involved in regulation of cell morphology and the actin cytoskeleton and interaction with actin capping protein.
  Mol Cell Biol, 25, 3519-3534.  
15743909 D.R.Kovar, J.Q.Wu, and T.D.Pollard (2005).
Profilin-mediated competition between capping protein and formin Cdc12p during cytokinesis in fission yeast.
  Mol Biol Cell, 16, 2313-2324.  
16143599 I.Delalle, C.M.Pfleger, E.Buff, P.Lueras, and I.K.Hariharan (2005).
Mutations in the Drosophila orthologs of the F-actin capping protein alpha- and beta-subunits cause actin accumulation and subsequent retinal degeneration.
  Genetics, 171, 1757-1765.  
15738427 J.L.Hodgkinson, C.Peters, S.A.Kuznetsov, and W.Steffen (2005).
Three-dimensional reconstruction of the dynactin complex by single-particle image analysis.
  Proc Natl Acad Sci U S A, 102, 3667-3672.  
15852055 W.M.Freeman, K.Brebner, S.G.Amara, M.S.Reed, J.Pohl, and A.G.Phillips (2005).
Distinct proteomic profiles of amphetamine self-administration transitional states.
  Pharmacogenomics J, 5, 203-214.  
14990563 E.S.Harris, F.Li, and H.N.Higgs (2004).
The mouse formin, FRLalpha, slows actin filament barbed end elongation, competes with capping protein, accelerates polymerization from monomers, and severs filaments.
  J Biol Chem, 279, 20076-20087.  
14657240 J.B.Moseley, I.Sagot, A.L.Manning, Y.Xu, M.J.Eck, D.Pellman, and B.L.Goode (2004).
A conserved mechanism for Bni1- and mDia1-induced actin assembly and dual regulation of Bni1 by Bud6 and profilin.
  Mol Biol Cell, 15, 896-907.  
14769858 K.Kim, A.Yamashita, M.A.Wear, Y.Maéda, and J.A.Cooper (2004).
Capping protein binding to actin in yeast: biochemical mechanism and physiological relevance.
  J Cell Biol, 164, 567-580.  
14736868 M.A.Wear, and J.A.Cooper (2004).
Capping protein binding to S100B: implications for the tentacle model for capping the actin filament barbed end.
  J Biol Chem, 279, 14382-14390.  
15362226 M.A.Wear, and J.A.Cooper (2004).
Capping protein: new insights into mechanism and regulation.
  Trends Biochem Sci, 29, 418-428.  
15282541 S.Falck, V.O.Paavilainen, M.A.Wear, J.G.Grossmann, J.A.Cooper, and P.Lappalainen (2004).
Biological role and structural mechanism of twinfilin-capping protein interaction.
  EMBO J, 23, 3010-3019.  
12796476 D.R.Kovar, J.R.Kuhn, A.L.Tichy, and T.D.Pollard (2003).
The fission yeast cytokinesis formin Cdc12p is a barbed end actin filament capping protein gated by profilin.
  J Cell Biol, 161, 875-887.  
12956956 M.A.Wear, A.Yamashita, K.Kim, Y.Maéda, and J.A.Cooper (2003).
How capping protein binds the barbed end of the actin filament.
  Curr Biol, 13, 1531-1537.  
12947123 S.Huang, L.Blanchoin, D.R.Kovar, and C.J.Staiger (2003).
Arabidopsis capping protein (AtCP) is a heterodimer that regulates assembly at the barbed ends of actin filaments.
  J Biol Chem, 278, 44832-44842.  
12860976 V.M.Fowler, N.J.Greenfield, and J.Moyer (2003).
Tropomodulin contains two actin filament pointed end-capping domains.
  J Biol Chem, 278, 40000-40009.  
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 code is shown on the right.