spacer
spacer

PDBsum entry 2p9u

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
2p9u
Jmol
Contents
Protein chains
398 a.a.
222 a.a. *
341 a.a. *
280 a.a. *
174 a.a. *
167 a.a. *
116 a.a. *
Ligands
ANP ×2
Metals
_CA ×2
Waters ×252
* Residue conservation analysis
PDB id:
2p9u
Name: Structural protein
Title: Crystal structure of bovine arp2/3 complex co-crystallized with amp-pnp and calcium
Structure: Actin-like protein 3. Chain: a. Synonym: actin-related protein 3. Engineered: yes. Actin-like protein 2. Chain: b. Synonym: actin-related protein 2. Engineered: yes. Actin-related protein 2/3 complex subunit 1b.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: actr3. Gene: actr2. Gene: arpc1b. Gene: arpc2. Gene: arpc3. Gene: arpc4.
Resolution:
2.75Å     R-factor:   0.219     R-free:   0.265
Authors: B.J.Nolen,T.D.Pollard
Key ref:
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. PubMed id: 17499050 DOI: 10.1016/j.molcel.2007.04.017
Date:
26-Mar-07     Release date:   29-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61157  (ARP3_BOVIN) -  Actin-related protein 3
Seq:
Struc:
418 a.a.
398 a.a.
Protein chain
Pfam   ArchSchema ?
A7MB62  (ARP2_BOVIN) -  Actin-related protein 2
Seq:
Struc:
394 a.a.
222 a.a.*
Protein chain
Pfam   ArchSchema ?
Q58CQ2  (ARC1B_BOVIN) -  Actin-related protein 2/3 complex subunit 1B
Seq:
Struc:
372 a.a.
341 a.a.*
Protein chain
Pfam   ArchSchema ?
Q3MHR7  (ARPC2_BOVIN) -  Actin-related protein 2/3 complex subunit 2
Seq:
Struc:
300 a.a.
280 a.a.
Protein chain
Pfam   ArchSchema ?
Q3T035  (ARPC3_BOVIN) -  Actin-related protein 2/3 complex subunit 3
Seq:
Struc:
178 a.a.
174 a.a.
Protein chain
Pfam   ArchSchema ?
Q148J6  (ARPC4_BOVIN) -  Actin-related protein 2/3 complex subunit 4
Seq:
Struc:
168 a.a.
167 a.a.
Protein chain
Pfam   ArchSchema ?
Q3SYX9  (ARPC5_BOVIN) -  Actin-related protein 2/3 complex subunit 5
Seq:
Struc:
151 a.a.
116 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     synapse   9 terms 
  Biological process     cell projection organization   10 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
DOI no: 10.1016/j.molcel.2007.04.017 Mol Cell 26:449-457 (2007)
PubMed id: 17499050  
 
 
Insights into the Influence of Nucleotides on Actin Family Proteins from Seven Structures of Arp2/3 Complex.
B.J.Nolen, T.D.Pollard.
 
  ABSTRACT  
 
ATP is required for nucleation of actin filament branches by Arp2/3 complex, but the influence of ATP binding and hydrolysis are poorly understood. We determined crystal structures of bovine Arp2/3 complex cocrystallized with various bound adenine nucleotides and cations. Nucleotide binding favors closure of the nucleotide-binding cleft of Arp3, but no large-scale conformational changes in the complex. Thus, ATP binding does not directly activate Arp2/3 complex but is part of a network of interactions that contribute to nucleation. We compared nucleotide-induced conformational changes of residues lining the cleft in Arp3 and actin structures to construct a movie depicting the proposed ATPase cycle for the actin family. Chemical crosslinking stabilized subdomain 1 of Arp2, revealing new electron density for 69 residues in this subdomain. Steric clashes with Arp3 appear to be responsible for intrinsic disorder of subdomains 1 and 2 of Arp2 in inactive Arp2/3 complex.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Nucleotide Binding Causes Changes in the Cleft of Arp3
(A) Superposition of Cα traces of apo-Arp2/3 complex (1K8K) and the ADP-cocrystallized, crosslinked Arp2/3 complex (2P9I). Structures were superposed by aligning subdomains 1 and 2 of Arp3. ARPC1, ARPC2, ARPC4, ARPC5, and Arp2 overlay well (both complexes gray). A rigid body motion of subdomains 3 and 4 of Arp3 and ARPC3 (cyan in ADP complex, red in apo complex) closes the cleft of structure 2P9I. Additional residues built for subdomain 1 in Arp2 of the crosslinked ADP cocrystals (2P9I) are also in cyan. ADP from 2P9I is yellow, and calcium is green.
(B) Stereo figure showing overlay of the nucleotide-binding cleft of Arp3 in the crosslinked ADP cocrystal (2P9I, cyan) and the crosslinked ATP cocrystal. (2P9K, yellow). ADP is magenta, and ATP is purple. Labeled residues mark key features: Thr14 for the P1 loop; Val174 for the P2 loop; and His80 for the sensor loop. Two distances define the width of the cleft: B1 (Thr14 Cα to Gly173 Cα; atoms shown as orange spheres) and B2 (Gly15 Cα to Asp172 Cα; atoms shown as brown spheres). Distance B2 was used to categorize clefts in structures of Arp2, Arp3, and actin as open, closed, or intermediate (Table 2).
(C) Stereo figure showing an overlay of the nucleotide-binding cleft of Arp3 in the crosslinked ADP cocrystal (2P9I, cyan protein, magenta ADP) and the previously published ADP-soaked structure (1U2V, orange protein, yellow ADP).
(D) Summary of conformational changes in the ATP-binding cleft during the ATPase cycle of actin family proteins. The dotted lines show hydrogen bonds between the γ-phosphate and the loops when the cleft is fully closed. Residue numbering is for bovine Arp3. Conformational changes observed in Arp3 and actin are numbered in red. Wavy red lines connect structural features that show correlated changes in one or more actin or Arp3 structures. (1) Two positions of a valine (Val174 in Arp3) in the P2 loop observed in Arp3 and actin structures suggest this valine may be involved in sensing the nucleotide-binding state. (2) A rotomer flip in Ser14 (Thr14 in Arp3) and a slight inward collapse (cyan arrowhead) of the P1 loop occur in the ADP-actin structures (1J6Z and 2HF4) and in a structure of Arp3 with bound ADP (2P9I). This movement is accompanied by a flip of the backbone carbonyl of a residue in the sensor loop in both Arp3 and actin. (3) Rigid body motions of subdomains 1 and 2 relative to subdomains 3 and 4 result in opening or closing of the nucleotide cleft. These structural changes have been observed in actin by comparing the single open structure (1HLU) to each of the other ADP- and ATP-containing structures, all of which are closed. Open and closed conformations have also been observed in Arp3, where the nucleotide state is correlated to the degree of opening of the cleft.
Figure 2.
Figure 2. Crosslinking Bovine Arp2/3 Complex Crystals with Glutaraldehyde Increases Order in Subdomain 1 of Arp2
(A) Final 3σ F[o] − F[c] electron density map and Cα trace of modeled regions of Arp2 in uncrosslinked bovine Arp2/3 complex-ATP-Mg^2+ cocrystals (2P9S). The map shows little density for subdomains 1 and 2.
(B) Final 3σ F[o] − F[c] omit map and Cσ trace of modeled regions of Arp2 in bovine Arp2/3 complex-ATP-Ca^2+ cocrystals treated with glutaraldehyde (2P9K). The newly modeled regions were not included in the map calculation.
(C) Steric hindrance with Arp3 may prevent Arp2 from closing in the inactive complex. Cα traces show Arp3 (cyan) and Arp2 (blue) from the structure of crosslinked ADP-Arp2/3 complex (2P9I) with the addition of a model of four disordered residues at the end of the αK/β15 loop of Arp3 (orange). Actin (red) is overlaid onto Arp2 to show potential clashes (red arrows) of subdomain 2 with the αI/αJ loop and the αK/β15 loop of Arp3. The yellow Cα trace (highlighted with arrow) shows how αK is connected to β15 in actin. The αK/β15 insert in Arp3 makes the αK helix three turns longer in Arp3 than actin.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 26, 449-457) copyright 2007.  

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.  
20946985 K.Murakami, T.Yasunaga, T.Q.Noguchi, Y.Gomibuchi, K.X.Ngo, T.Q.Uyeda, and T.Wakabayashi (2010).
Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
  Cell, 143, 275-287.
PDB codes: 3a5l 3a5m 3a5n 3a5o 3g37
20096561 R.Dominguez (2010).
Structural insights into de novo actin polymerization.
  Curr Opin Struct Biol, 20, 217-225.  
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
19620726 J.Pfaendtner, D.Branduardi, M.Parrinello, T.D.Pollard, and G.A.Voth (2009).
Nucleotide-dependent conformational states of actin.
  Proc Natl Acad Sci U S A, 106, 12723-12728.  
19874150 R.Dominguez (2009).
Actin filament nucleation and elongation factors--structure-function relationships.
  Crit Rev Biochem Mol Biol, 44, 351-366.  
18940808 T.D.Pollard, and J.Berro (2009).
Mathematical models and simulations of cellular processes based on actin filaments.
  J Biol Chem, 284, 5433-5437.  
19158791 T.Oda, M.Iwasa, T.Aihara, Y.Maéda, and A.Narita (2009).
The nature of the globular- to fibrous-actin transition.
  Nature, 457, 441-445.
PDB code: 2zwh
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
18165685 C.C.Beltzner, and T.D.Pollard (2008).
Pathway of actin filament branch formation by Arp2/3 complex.
  J Biol Chem, 283, 7135-7144.  
18708324 G.M.Altschuler, and K.R.Willison (2008).
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin.
  J R Soc Interface, 5, 1391-1408.  
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.  
18805923 J.Pfaendtner, and G.A.Voth (2008).
Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex.
  Biophys J, 95, 5324-5333.  
18316414 L.Cai, and J.E.Bear (2008).
Peering deeply inside the branch.
  J Cell Biol, 180, 853-855.  
18462674 M.Boczkowska, G.Rebowski, M.V.Petoukhov, D.B.Hayes, D.I.Svergun, and R.Dominguez (2008).
X-ray scattering study of activated Arp2/3 complex with bound actin-WCA.
  Structure, 16, 695-704.  
17873883 A.Orlova, E.C.Garner, V.E.Galkin, J.Heuser, R.D.Mullins, and E.H.Egelman (2007).
The structure of bacterial ParM filaments.
  Nat Struct Mol Biol, 14, 921-926.
PDB code: 2qu4
17965017 E.Reisler, and E.H.Egelman (2007).
Actin structure and function: what we still do not understand.
  J Biol Chem, 282, 36133-36137.  
17704151 J.W.Chu, and G.A.Voth (2007).
Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.
  Biophys J, 93, 3860-3871.  
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.