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PDBsum entry 1tyq
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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
1tyq

 

 

 

 

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Contents
Protein chains
399 a.a.
208 a.a. *
342 a.a. *
274 a.a. *
169 a.a. *
166 a.a. *
134 a.a. *
Ligands
ATP ×2
Metals
_CA ×2
Waters ×181
* Residue conservation analysis
PDB id:
1tyq
Name: Structural protein
Title: Crystal structure of arp2/3 complex with bound atp and calcium
Structure: Actin-related protein 3. Chain: a. Synonym: actin-like protein 3, actin-2. Actin-related protein 2. Chain: b. Arp2/3 complex 41kda subunit. Chain: c. Arp2/3 complex 34kda subunit. Chain: d.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: thymus
Biol. unit: Heptamer (from PQS)
Resolution:
2.55Å     R-factor:   0.232     R-free:   0.272
Authors: B.J.Nolen,R.S.Littlefield,T.D.Pollard
Key ref:
B.J.Nolen et al. (2004). Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP. Proc Natl Acad Sci U S A, 101, 15627-15632. PubMed id: 15505213 DOI: 10.1073/pnas.0407149101
Date:
08-Jul-04     Release date:   09-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61157  (ARP3_BOVIN) -  Actin-related protein 3 from Bos taurus
Seq:
Struc: 		418 a.a.
399 a.a.
Protein chain
Pfam   ArchSchema ?
A7MB62  (ARP2_BOVIN) -  Actin-related protein 2 from Bos taurus
Seq:
Struc: 		394 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q58CQ2  (ARC1B_BOVIN) -  Actin-related protein 2/3 complex subunit 1B from Bos taurus
Seq:
Struc: 		372 a.a.
342 a.a.*
Protein chain
Pfam   ArchSchema ?
Q3MHR7  (ARPC2_BOVIN) -  Actin-related protein 2/3 complex subunit 2 from Bos taurus
Seq:
Struc: 		300 a.a.
274 a.a.
Protein chain
Pfam   ArchSchema ?
Q3T035  (ARPC3_BOVIN) -  Actin-related protein 2/3 complex subunit 3 from Bos taurus
Seq:
Struc: 		178 a.a.
169 a.a.
Protein chain
Pfam   ArchSchema ?
Q148J6  (ARPC4_BOVIN) -  Actin-related protein 2/3 complex subunit 4 from Bos taurus
Seq:
Struc: 		168 a.a.
166 a.a.
Protein chain
Pfam   ArchSchema ?
Q3SYX9  (ARPC5_BOVIN) -  Actin-related protein 2/3 complex subunit 5 from Bos taurus
Seq:
Struc: 		151 a.a.
134 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1073/pnas.0407149101 Proc Natl Acad Sci U S A 101:15627-15632 (2004)
PubMed id: 15505213  
 
 
Crystal structures of actin-related protein 2/3 complex with bound ATP or ADP.
B.J.Nolen, R.S.Littlefield, T.D.Pollard.
 
  ABSTRACT  
 
Actin-related protein (Arp) 2/3 complex stimulates formation of actin filaments at the leading edge of motile cells. Nucleation of filaments depends on hydrolysis of ATP bound to Arp2. Here we report crystal structures of Arp2/3 complex with bound ATP or ADP. The nucleotides are immobilized on the face of subdomains 3 and 4 of Arp2, whereas subdomains 1 and 2 are flexible and absent from the electron density maps. This flexibility may explain why Arp2 does not hydrolyze ATP until the complex is activated. ATP stabilizes a relatively closed conformation of Arp3 with the gamma-phosphate bridging loops from opposite sides of the cleft. ADP binds Arp3 in a unique conformation that favors an open cleft, revealing a conformational change that may occur in actin and Arps when ATP is hydrolyzed and phosphate dissociates. These structures provide the an opportunity to compare all nucleotide-binding states in an actin-related protein and give insights into the function of both the Arp2/3 complex and actin.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Stereo figure showing conformational changes cased by ATP binding. (A) Overlay of subdomains 1 and 2 of Arp3 from the apo-(red) and ATP (blue) complexes. (B) Overlay of Arp3 based on the superposition of the entire Arp3 subunits from Apo-containing (red), ADP-containing (blue), and ATP-containing (cyan) complexes. ATP is shown in yellow. DYNDOM-defined rotation axes required to bring the apo-Arp3 in alignment with each of the nucleotide-containing structures are blue for ADP-Arp3 and green for ATP-Arp3. The dotted black lines indicate distances measured to compare cleft closure. Lengths in Å of A-C are as follows: apo-Arp3, 9.84, 8.47, and 16.08; ADP-Arp3, 8.28, 8.84, and 15.02; ATP-Arp3, 8.35, 6.75, and 13.10; actin (PDB entry 1ATN [PDB] ), 8.35, 5.49, and 10.36. The coordinate error estimate by Luzzati plot is 0.36 Å for the ADP complex and 0.38 Å for the ATP complex (44). 		Figure 5.
Fig. 5. Nucleotide binding to Arp3. (A) Overlay of Arp3 from ATP (yellow) and ADP-Arp2/3 (cyan) complexes based on the superposition of the entire Arp3 subunit (as in Fig. 3B). ADP is shown in magenta, and ATP is shown in blue. (B) Interactions of ATP phosphates with Arp3. (C) Interactions of ADP phosphates with Arp3. (D) Overlay of actin (PDB entry 1NMD [PDB] , green) and ATP-Arp3 (yellow) based on superposition of the entire molecules. ATP and divalent cation from the actin structure are orange, ATP and Ca^2+ from Arp3 are blue. Select water molecules from 1NMD [PDB] are modeled as red spheres.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20404198 E.D.Goley, A.Rammohan, E.A.Znameroski, E.N.Firat-Karalar, D.Sept, and M.D.Welch (2010).
An actin-filament-binding interface on the Arp2/3 complex is critical for nucleation and branch stability.
  Proc Natl Acad Sci U S A, 107, 8159-8164.  
20237478 K.G.Campellone, and M.D.Welch (2010).
A nucleator arms race: cellular control of actin assembly.
  Nat Rev Mol Cell Biol, 11, 237-251.  
19602153 A.I.Derman, E.C.Becker, B.D.Truong, A.Fujioka, T.M.Tucey, M.L.Erb, P.C.Patterson, and J.Pogliano (2009).
Phylogenetic analysis identifies many uncharacterized actin-like proteins (Alps) in bacteria: regulated polymerization, dynamic instability and treadmilling in Alp7A.
  Mol Microbiol, 73, 534-552.  
19648907 B.J.Nolen, N.Tomasevic, A.Russell, D.W.Pierce, Z.Jia, C.D.McCormick, J.Hartman, R.Sakowicz, and T.D.Pollard (2009).
Characterization of two classes of small molecule inhibitors of Arp2/3 complex.
  Nature, 460, 1031-1034.
PDB codes: 3dxk 3dxm
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.  
19233204 K.Lasker, M.Topf, A.Sali, and H.J.Wolfson (2009).
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.
  J Mol Biol, 388, 180-194.  
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.  
19298826 W.D.Zencheck, H.Xiao, B.J.Nolen, R.H.Angeletti, T.D.Pollard, and S.C.Almo (2009).
Nucleotide- and activator-dependent structural and dynamic changes of arp2/3 complex monitored by hydrogen/deuterium exchange and mass spectrometry.
  J Mol Biol, 390, 414-427.  
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
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.  
18725535 L.L.LeClaire, M.Baumgartner, J.H.Iwasa, R.D.Mullins, and D.L.Barber (2008).
Phosphorylation of the Arp2/3 complex is necessary to nucleate actin filaments.
  J Cell Biol, 182, 647-654.  
17499050 B.J.Nolen, and T.D.Pollard (2007).
Insights into the influence of nucleotides on actin family proteins from seven structures of Arp2/3 complex.
  Mol Cell, 26, 449-457.
PDB codes: 2p9i 2p9k 2p9l 2p9n 2p9p 2p9s 2p9u
17391512 I.M.Sehring, J.Mansfeld, C.Reiner, E.Wagner, H.Plattner, and R.Kissmehl (2007).
The actin multigene family of Paramecium tetraurelia.
  BMC Genomics, 8, 82.  
17251352 J.G.Kiselar, R.Mahaffy, T.D.Pollard, S.C.Almo, and M.R.Chance (2007).
Visualizing Arp2/3 complex activation mediated by binding of ATP and WASp using structural mass spectrometry.
  Proc Natl Acad Sci U S A, 104, 1552-1557.  
17477841 T.D.Pollard (2007).
Regulation of actin filament assembly by Arp2/3 complex and formins.
  Annu Rev Biophys Biomol Struct, 36, 451-477.  
16880808 D.R.Kovar (2006).
Arp2/3 ATP hydrolysis: to branch or to debranch?
  Nat Cell Biol, 8, 783-785.  
16990851 E.D.Goley, and M.D.Welch (2006).
The ARP2/3 complex: an actin nucleator comes of age.
  Nat Rev Mol Cell Biol, 7, 713-726.  
15741975 A.H.Aguda, L.D.Burtnick, and R.C.Robinson (2005).
The state of the filament.
  EMBO Rep, 6, 220-226.  
16262445 C.Egile, I.Rouiller, X.P.Xu, N.Volkmann, R.Li, and D.Hanein (2005).
Mechanism of filament nucleation and branch stability revealed by the structure of the Arp2/3 complex at actin branch junctions.
  PLoS Biol, 3, e383.  
16195354 J.Muller, Y.Oma, L.Vallar, E.Friederich, O.Poch, and B.Winsor (2005).
Sequence and comparative genomic analysis of actin-related proteins.
  Mol Biol Cell, 16, 5736-5748.  
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.

 

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