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PDBsum entry 1t44

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
1t44
Jmol
Contents
Protein chains
144 a.a. *
358 a.a. *
Ligands
ATP
Metals
_CA ×3
Waters ×427
* Residue conservation analysis
PDB id:
1t44
Name: Structural protein
Title: Structural basis of actin sequestration by thymosin-b4: implications for arp2/3 activation
Structure: Chimera of gelsolin domain 1 and c-terminal domain of thymosin beta-4. Chain: g. Fragment: chimera of gelsolin domain 1 (residues 28-152) from human and c-terminal domain of thymosin beta-4 from mouse (residues 153-171). Engineered: yes. Actin, alpha. Chain: a.
Source: Homo sapiens, mus musculus. Human, house mouse. Organism_taxid: 9606,10090. Strain: ,. Expressed in: escherichia coli. Expression_system_taxid: 562. Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.147     R-free:   0.195
Authors: E.Irobi,A.H.Aguda,M.Larsson,L.D.Burtnick,R.C.Robinson
Key ref:
E.Irobi et al. (2004). Structural basis of actin sequestration by thymosin-beta4: implications for WH2 proteins. EMBO J, 23, 3599-3608. PubMed id: 15329672 DOI: 10.1038/sj.emboj.7600372
Date:
28-Apr-04     Release date:   07-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06396  (GELS_HUMAN) -  Gelsolin
Seq:
Struc:
 
Seq:
Struc:
782 a.a.
144 a.a.*
Protein chain
Pfam   ArchSchema ?
P68135  (ACTS_RABIT) -  Actin, alpha skeletal muscle
Seq:
Struc:
377 a.a.
358 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 18 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     cytoskeleton organization   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1038/sj.emboj.7600372 EMBO J 23:3599-3608 (2004)
PubMed id: 15329672  
 
 
Structural basis of actin sequestration by thymosin-beta4: implications for WH2 proteins.
E.Irobi, A.H.Aguda, M.Larsson, C.Guerin, H.L.Yin, L.D.Burtnick, L.Blanchoin, R.C.Robinson.
 
  ABSTRACT  
 
The WH2 (Wiscott-Aldridge syndrome protein homology domain 2) repeat is an actin interacting motif found in monomer sequestering and filament assembly proteins. We have stabilized the prototypical WH2 family member, thymosin-beta4 (Tbeta4), with respect to actin, by creating a hybrid between gelsolin domain 1 and the C-terminal half of Tbeta4 (G1-Tbeta4). This hybrid protein sequesters actin monomers, severs actin filaments and acts as a leaky barbed end cap. Here, we present the structure of the G1-Tbeta4:actin complex at 2 A resolution. The structure reveals that Tbeta4 sequesters by capping both ends of the actin monomer, and that exchange of actin between Tbeta4 and profilin is mediated by a minor overlap in binding sites. The structure implies that multiple WH2 motif-containing proteins will associate longitudinally with actin filaments. Finally, we discuss the role of the WH2 motif in arp2/3 activation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 T 4 interactions with G-actin. (A) Structure of the G1-T 4:actin complex. The actin protomer is shown in sky blue with a bound ATP in orange (ball-and-stick representation) and a calcium ion (green sphere). The actin subdomains are labeled 1 -4. The G1 portion of the hybrid (residues 27 -149) is shown in royal blue with two associated calcium ions (dark spheres). The T 4 portion (residues 21 -39) is depicted in gold. The red region of the G1-T 4 ribbon represents the G1 sequence that is homologous to the T 4 sequence (residues 17 -20 in T 4). (B) A 90 rotation (clockwise when viewed from above) around the vertical axis compared to (A). (C) Model of T 4 bound to actin. Actin and T 4 residues 17 -39 are taken from the structure in (B). The T 4 N-terminus (pink) is modeled by taking the homologous amino acids from the ciboulot:actin structure (PDB code 1SQK; Hertzog et al, 2004) after superimposing the actin structures. (D) Stereo view of the structural overlap within the LKKTET-related motif between the actin-bound forms of G1-T 4 and ciboulot. The actin structures from the present structure and the ciboulot:actin structure (PDB code 1SQK; Hertzog et al, 2004) were superimposed. Gelsolin (G) residues Phe149-Lys150-His151-Val152 and T 4 (T) residue Glu21 from the hybrid are shown in green and are labeled in the left panel. The homologous ciboulot (C) residues Leu30-Lys31-Asn32-Ala33-Ser34 are shown in pink and are labeled in the right panel.
Figure 5.
Figure 5 Competition for the T 4 actin-binding site. (A) Model of the competition between T 4 and DNase I for binding actin. The structure of actin:DNase I (PDB code 1ATN; Kabsch et al, 1990) and the T 4:actin model are superimposed, with only one actin shown. DNase I is drawn in red. The arrow indicates a structural clash. (B) Model of the competition between T 4 and profilin for binding actin. The structure of profilin:actin (PDB code 2BTF; Schutt et al, 1993) has been superimposed on the T 4:actin model, and profilin is depicted in red. The arrow indicates a structural clash. (C) Model of the interactions of the WH2 domain family with F-actin. T 4 docked onto the side of an actin filament based on superimposing the actins from two copies of the T 4:actin model (Figure 2C) on two actins from a modified version of the Holmes model of the filament (Holmes et al, 1990). The actins are colored sky blue and T 4s are painted as in Figure 2A. This representation shows that capping by the N-terminal helix and the minus-end capping helix prevent the T 4:actin complex from joining either end of a filament. The model also demonstrates that multiple WH2 repeat proteins will bind actin protomers in a longitudinal manner, along the axis of the filament.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 3599-3608) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21072628 A.E.Lang, G.Schmidt, J.J.Sheets, and K.Aktories (2011).
Targeting of the actin cytoskeleton by insecticidal toxins from Photorhabdus luminescens.
  Naunyn Schmiedebergs Arch Pharmacol, 383, 227-235.  
20185726 A.E.Lang, G.Schmidt, A.Schlosser, T.D.Hey, I.M.Larrinua, J.J.Sheets, H.G.Mannherz, and K.Aktories (2010).
Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering.
  Science, 327, 1139-1142.  
20538977 A.M.Ducka, P.Joel, G.M.Popowicz, K.M.Trybus, M.Schleicher, A.A.Noegel, R.Huber, T.A.Holak, and T.Sitar (2010).
Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation.
  Proc Natl Acad Sci U S A, 107, 11757-11762.
PDB codes: 3mmv 3mn5 3mn6 3mn7 3mn9
20536449 C.Husson, F.X.Cantrelle, P.Roblin, D.Didry, K.H.Le, J.Perez, E.Guittet, C.Van Heijenoort, L.Renault, and M.F.Carlier (2010).
Multifunctionality of the beta-thymosin/WH2 module: G-actin sequestration, actin filament growth, nucleation, and severing.
  Ann N Y Acad Sci, 1194, 44-52.  
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.  
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.  
20529303 S.Koshikawa, R.Cornette, T.Matsumoto, and T.Miura (2010).
The homolog of Ciboulot in the termite (Hodotermopsis sjostedti): a multimeric beta-thymosin involved in soldier-specific morphogenesis.
  BMC Dev Biol, 10, 63.  
19406642 B.Qualmann, and M.M.Kessels (2009).
New players in actin polymerization--WH2-domain-containing actin nucleators.
  Trends Cell Biol, 19, 276-285.  
19405116 H.G.Mannherz, and E.Hannappel (2009).
The beta-thymosins: intracellular and extracellular activities of a versatile actin binding protein family.
  Cell Motil Cytoskeleton, 66, 839-851.  
19260013 P.Tompa, M.Fuxreiter, C.J.Oldfield, I.Simon, A.K.Dunker, and V.N.Uversky (2009).
Close encounters of the third kind: disordered domains and the interactions of proteins.
  Bioessays, 31, 328-335.  
19874150 R.Dominguez (2009).
Actin filament nucleation and elongation factors--structure-function relationships.
  Crit Rev Biochem Mol Biol, 44, 351-366.  
19289059 R.Kardos, K.Pozsonyi, E.Nevalainen, P.Lappalainen, M.Nyitrai, and G.Hild (2009).
The effects of ADF/cofilin and profilin on the conformation of the ATP-binding cleft of monomeric actin.
  Biophys J, 96, 2335-2343.  
19909017 S.Sribenja, M.Li, S.Wongkham, C.Wongkham, Q.Yao, and C.Chen (2009).
Advances in thymosin beta10 research: differential expression, molecular mechanisms, and clinical implications in cancer and other conditions.
  Cancer Invest, 27, 1016-1022.  
19460343 Y.Fan, Y.Gong, P.K.Ghosh, L.M.Graham, and P.L.Fox (2009).
Spatial coordination of actin polymerization and ILK-Akt2 activity during endothelial cell migration.
  Dev Cell, 16, 661-674.  
18640983 B.J.Nolen, and T.D.Pollard (2008).
Structure and biochemical properties of fission yeast Arp2/3 complex lacking the Arp2 subunit.
  J Biol Chem, 283, 26490-26498.
PDB code: 3dwl
18669664 G.Rebowski, M.Boczkowska, D.B.Hayes, L.Guo, T.C.Irving, and R.Dominguez (2008).
X-ray scattering study of actin polymerization nuclei assembled by tandem W domains.
  Proc Natl Acad Sci U S A, 105, 10785-10790.  
18327913 J.K.Au, A.O.Olivares, A.Henn, W.Cao, D.Safer, and E.M.De La Cruz (2008).
Widely distributed residues in thymosin beta4 are critical for actin binding.
  Biochemistry, 47, 4181-4188.  
17468228 B.Xue, A.H.Aguda, and R.C.Robinson (2007).
Models of the actin-bound forms of the beta-thymosins.
  Ann N Y Acad Sci, 1112, 56-66.  
17495248 H.Q.Sun, and H.L.Yin (2007).
The beta-thymosin enigma.
  Ann N Y Acad Sci, 1112, 45-55.  
17468230 J.K.Au, E.M.De La Cruz, and D.Safer (2007).
Contributions from all over: widely distributed residues in thymosin beta-4 affect the kinetics and stability of actin binding.
  Ann N Y Acad Sci, 1112, 38-44.  
18042452 M.Bosch, K.H.Le, B.Bugyi, J.J.Correia, L.Renault, and M.F.Carlier (2007).
Analysis of the function of Spire in actin assembly and its synergy with formin and profilin.
  Mol Cell, 28, 555-568.  
17947587 M.F.Carlier, M.Hertzog, D.Didry, L.Renault, F.X.Cantrelle, C.van Heijenoort, M.Knossow, and E.Guittet (2007).
Structure, function, and evolution of the beta-thymosin/WH2 (WASP-Homology2) actin-binding module.
  Ann N Y Acad Sci, 1112, 67-75.  
17947590 P.Popoli, R.Pepponi, A.Martire, M.Armida, A.Pèzzola, M.Galluzzo, M.R.Domenici, R.L.Potenza, M.T.Tebano, C.Mollinari, D.Merlo, and E.Garaci (2007).
Neuroprotective effects of thymosin beta4 in experimental models of excitotoxicity.
  Ann N Y Acad Sci, 1112, 219-224.  
17348036 P.Qiu, M.Kurpakus-Wheater, and G.Sosne (2007).
Matrix metalloproteinase activity is necessary for thymosin beta 4 promotion of epithelial cell migration.
  J Cell Physiol, 212, 165-173.  
17956734 R.Ahuja, R.Pinyol, N.Reichenbach, L.Custer, J.Klingensmith, M.M.Kessels, and B.Qualmann (2007).
Cordon-bleu is an actin nucleation factor and controls neuronal morphology.
  Cell, 131, 337-350.  
17468236 R.Dominguez (2007).
The beta-thymosin/WH2 fold: multifunctionality and structure.
  Ann N Y Acad Sci, 1112, 86-94.  
17292833 S.H.Lee, F.Kerff, D.Chereau, F.Ferron, A.Klug, and R.Dominguez (2007).
Structural basis for the actin-binding function of missing-in-metastasis.
  Structure, 15, 145-155.
PDB codes: 2d1k 2d1l
16403731 A.E.Kelly, H.Kranitz, V.Dötsch, and R.D.Mullins (2006).
Actin binding to the central domain of WASP/Scar proteins plays a critical role in the activation of the Arp2/3 complex.
  J Biol Chem, 281, 10589-10597.  
16531231 A.H.Aguda, B.Xue, E.Irobi, T.Préat, and R.C.Robinson (2006).
The structural basis of actin interaction with multiple WH2/beta-thymosin motif-containing proteins.
  Structure, 14, 469-476.
PDB codes: 2ff3 2ff6
16757474 A.Pelikan Conchaudron, D.Didry, K.H.Le, E.Larquet, N.Boisset, D.Pantaloni, and M.F.Carlier (2006).
Analysis of tetramethylrhodamine-labeled actin polymerization and interaction with actin regulatory proteins.
  J Biol Chem, 281, 24036-24047.  
16542844 E.G.Yarmola, and M.R.Bubb (2006).
Profilin: emerging concepts and lingering misconceptions.
  Trends Biochem Sci, 31, 197-205.  
16272441 I.V.Dedova, O.P.Nikolaeva, D.Safer, E.M.De La Cruz, and C.G.dos Remedios (2006).
Thymosin beta4 induces a conformational change in actin monomers.
  Biophys J, 90, 985-992.  
16569662 P.A.Loomis, A.E.Kelly, L.Zheng, B.Changyaleket, G.Sekerková, E.Mugnaini, A.Ferreira, R.D.Mullins, and J.R.Bartles (2006).
Targeted wild-type and jerker espins reveal a novel, WH2-domain-dependent way to make actin bundles in cells.
  J Cell Sci, 119, 1655-1665.  
17012745 R.S.Fischer, E.G.Yarmola, K.L.Weber, K.D.Speicher, D.W.Speicher, M.R.Bubb, and V.M.Fowler (2006).
Tropomodulin 3 binds to actin monomers.
  J Biol Chem, 281, 36454-36465.  
15741975 A.H.Aguda, L.D.Burtnick, and R.C.Robinson (2005).
The state of the filament.
  EMBO Rep, 6, 220-226.  
15854898 B.Baum, and P.Kunda (2005).
Actin nucleation: spire - actin nucleator in a class of its own.
  Curr Biol, 15, R305-R308.  
16275905 D.Chereau, F.Kerff, P.Graceffa, Z.Grabarek, K.Langsetmo, and R.Dominguez (2005).
Actin-bound structures of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 and the implications for filament assembly.
  Proc Natl Acad Sci U S A, 102, 16644-16649.
PDB codes: 2a3z 2a40 2a41 2a42
15674283 M.E.Quinlan, J.E.Heuser, E.Kerkhoff, and R.D.Mullins (2005).
Drosophila Spire is an actin nucleation factor.
  Nature, 433, 382-388.  
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.