7PDZ

Structure of capping protein bound to the barbed end of a cytoplasmic actin filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks.

Funk, J.Merino, F.Schaks, M.Rottner, K.Raunser, S.Bieling, P.

(2021) Nat Commun 12: 5329-5329

  • DOI: https://doi.org/10.1038/s41467-021-25682-5
  • Primary Citation of Related Structures:  
    7PDZ

  • PubMed Abstract: 

    Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside from terminating filament growth, CP potentiates the nucleation of actin filaments by the Arp2/3 complex in branched actin networks through an unclear mechanism. Here, we combine structural biology with in vitro reconstitution to demonstrate that CP not only terminates filament elongation, but indirectly stimulates the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association to filament barbed ends. Key to this function is one of CP's C-terminal "tentacle" extensions, which sterically masks the main interaction site of the terminal actin protomer. Deletion of the β tentacle only modestly impairs capping. However, in the context of a growing branched actin network, its removal potently inhibits nucleation promoting factors by tethering them to capped filament ends. End tethering of NPFs prevents their loading with actin monomers required for activation of the Arp2/3 complex and thus strongly inhibits branched network assembly both in cells and reconstituted motility assays. Our results mechanistically explain how CP couples two opposed processes-capping and nucleation-in branched actin network assembly.


  • Organizational Affiliation

    Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of F-actin-capping protein subunit betaA [auth E]272Mus musculusMutation(s): 0 
Gene Names: CapzbCappb1
UniProt & NIH Common Fund Data Resources
Find proteins for P47757 (Mus musculus)
Explore P47757 
Go to UniProtKB:  P47757
IMPC:  MGI:104652
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47757
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin-capping protein subunit alpha-1B [auth F]286Mus musculusMutation(s): 0 
Gene Names: Capza1Cappa1
UniProt & NIH Common Fund Data Resources
Find proteins for P47753 (Mus musculus)
Explore P47753 
Go to UniProtKB:  P47753
IMPC:  MGI:106227
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47753
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Bos taurusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P60712 (Bos taurus)
Explore P60712 
Go to UniProtKB:  P60712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60712
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PhalloidinI [auth Q],
J [auth R],
K [auth S],
L [auth T],
M [auth P]
7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth O]
N [auth I]
P [auth J]
S [auth K]
U [auth L]
AA [auth O],
N [auth I],
P [auth J],
S [auth K],
U [auth L],
X [auth N]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth O],
R [auth K],
W [auth L],
Z [auth N]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth O]
O [auth I]
Q [auth J]
T [auth K]
V [auth L]
BA [auth O],
O [auth I],
Q [auth J],
T [auth K],
V [auth L],
Y [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
C [auth I]
D [auth J]
E [auth K]
F [auth L]
G [auth N]
C [auth I],
D [auth J],
E [auth K],
F [auth L],
G [auth N],
H [auth O]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
HYP
Query on HYP
I [auth Q],
J [auth R],
K [auth S],
L [auth T],
M [auth P]
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPHIRE1.3
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references