3AA1

Crystal structure of Actin capping protein in complex with the Cp-binding motif derived from CKIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition

Takeda, S.Minakata, S.Koike, R.Kawahata, I.Narita, A.Kitazawa, M.Ota, M.Yamakuni, T.Maeda, Y.Nitanai, Y.

(2010) PLoS Biol 8: e1000416-e1000416

  • DOI: 10.1371/journal.pbio.1000416
  • Primary Citation of Related Structures:  
    3AA0, 3AA1, 3AA6, 3AA7, 3AAA

  • PubMed Abstract: 
  • The actin capping protein (CP) tightly binds to the barbed end of actin filaments, thus playing a key role in actin-based lamellipodial dynamics. V-1 and CARMIL proteins directly bind to CP and inhibit the filament capping activity of CP. V-1 completely inhibits CP from interacting with the barbed end, whereas CARMIL proteins act on the barbed end-bound CP and facilitate its dissociation from the filament (called uncapping activity) ...

    The actin capping protein (CP) tightly binds to the barbed end of actin filaments, thus playing a key role in actin-based lamellipodial dynamics. V-1 and CARMIL proteins directly bind to CP and inhibit the filament capping activity of CP. V-1 completely inhibits CP from interacting with the barbed end, whereas CARMIL proteins act on the barbed end-bound CP and facilitate its dissociation from the filament (called uncapping activity). Previous studies have revealed the striking functional differences between the two regulators. However, the molecular mechanisms describing how these proteins inhibit CP remains poorly understood. Here we present the crystal structures of CP complexed with V-1 and with peptides derived from the CP-binding motif of CARMIL proteins (CARMIL, CD2AP, and CKIP-1). V-1 directly interacts with the primary actin binding surface of CP, the C-terminal region of the alpha-subunit. Unexpectedly, the structures clearly revealed the conformational flexibility of CP, which can be attributed to a twisting movement between the two domains. CARMIL peptides in an extended conformation interact simultaneously with the two CP domains. In contrast to V-1, the peptides do not directly compete with the barbed end for the binding surface on CP. Biochemical assays revealed that the peptides suppress the interaction between CP and V-1, despite the two inhibitors not competing for the same binding site on CP. Furthermore, a computational analysis using the elastic network model indicates that the interaction of the peptides alters the intrinsic fluctuations of CP. Our results demonstrate that V-1 completely sequesters CP from the barbed end by simple steric hindrance. By contrast, CARMIL proteins allosterically inhibit CP, which appears to be a prerequisite for the uncapping activity. Our data suggest that CARMIL proteins down-regulate CP by affecting its conformational dynamics. This conceptually new mechanism of CP inhibition provides a structural basis for the regulation of the barbed end elongation in cells.


    Organizational Affiliation

    Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan. takeda.shuichi@f.mbox.nagoya-u.ac.jp



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-actin-capping protein subunit alpha-1A286Gallus gallusMutation(s): 0 
Gene Names: CAPZA1
UniProt
Find proteins for P13127 (Gallus gallus)
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Go to UniProtKB:  P13127
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
F-actin-capping protein subunit beta isoforms 1 and 2B244Gallus gallusMutation(s): 0 
Gene Names: CAPZB
UniProt
Find proteins for P14315 (Gallus gallus)
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
23mer peptide from Pleckstrin homology domain-containing family O member 1C23Homo sapiensMutation(s): 0 
Gene Names: PLEKHO1CKIP1OC120HQ0024c
UniProt & NIH Common Fund Data Resources
Find proteins for Q53GL0 (Homo sapiens)
Explore Q53GL0 
Go to UniProtKB:  Q53GL0
PHAROS:  Q53GL0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.315α = 90
b = 66.298β = 90
c = 136.666γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance