3DXM

Structure of Bos taurus Arp2/3 Complex with Bound Inhibitor CK0993548


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

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Literature

Characterization of two classes of small molecule inhibitors of Arp2/3 complex

Nolen, B.J.Tomasevic, N.Russell, A.Pierce, D.W.Jia, Z.McCormick, C.D.Hartman, J.Sakowicz, R.Pollard, T.D.

(2009) Nature 460: 1031-1034

  • DOI: https://doi.org/10.1038/nature08231
  • Primary Citation of Related Structures:  
    3DXK, 3DXM

  • PubMed Abstract: 
  • Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells ...

    Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells. Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments. CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation. CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation. Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes. Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells.


    Organizational Affiliation

    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
UniProt
Find proteins for P61157 (Bos taurus)
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Go to UniProtKB:  P61157
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UniProt GroupP61157
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
UniProt
Find proteins for A7MB62 (Bos taurus)
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UniProt GroupA7MB62
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
UniProt
Find proteins for Q58CQ2 (Bos taurus)
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UniProt GroupQ58CQ2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
Gene Names: ARPC2
UniProt
Find proteins for Q3MHR7 (Bos taurus)
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UniProt GroupQ3MHR7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
Gene Names: ARPC3
UniProt
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
Gene Names: ARPC4
UniProt
Find proteins for Q148J6 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
Gene Names: ARPC5
UniProt
Find proteins for Q3SYX9 (Bos taurus)
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UniProt GroupQ3SYX9
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N24
Query on N24

Download Ideal Coordinates CCD File 
H [auth A](2S)-2-(3-bromophenyl)-3-(5-chloro-2-hydroxyphenyl)-1,3-thiazolidin-4-one
C15 H11 Br Cl N O2 S
KEGQNJITMFBVAC-HNNXBMFYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
N24 PDBBind:  3DXM Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.383α = 90
b = 129.651β = 90
c = 203.787γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description