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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 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 fila ...

    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 3A418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
Find proteins for P61157 (Bos taurus)
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Go to UniProtKB:  P61157
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2B394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
Find proteins for A7MB62 (Bos taurus)
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BC372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2D300Bos taurusMutation(s): 0 
Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus)
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3E178Bos taurusMutation(s): 0 
Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4F168Bos taurusMutation(s): 0 
Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5G151Bos taurusMutation(s): 0 
Gene Names: ARPC5
Find proteins for Q3SYX9 (Bos taurus)
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N24
Query on N24

Download CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N24Kd :  1000   nM  PDBBind
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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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance