6DJN

Cryo-EM structure of ADP-Pi-actin filaments


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanism of actin polymerization revealed by cryo-EM structures of actin filaments with three different bound nucleotides.

Chou, S.Z.Pollard, T.D.

(2019) Proc. Natl. Acad. Sci. U.S.A. --: --

  • DOI: 10.1073/pnas.1807028115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-P <sub>i </sub> (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolutio ...

    We used cryo-electron microscopy (cryo-EM) to reconstruct actin filaments with bound AMPPNP (β,γ-imidoadenosine 5'-triphosphate, an ATP analog, resolution 3.1 Å), ADP-P i (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolution 3.6 Å). Subunits in the three filaments have similar backbone conformations, so assembly rather than ATP hydrolysis or phosphate dissociation is responsible for their flattened conformation in filaments. Polymerization increases the rate of ATP hydrolysis by changing the positions of the side chains of Q137 and H161 in the active site. Flattening during assembly also promotes interactions along both the long-pitch and short-pitch helices. In particular, conformational changes in subdomain 3 open up multiple favorable interactions with the DNase-I binding loop in subdomain 2 of the adjacent subunit. Subunits at the barbed end of the filament are likely to be in this favorable conformation, while monomers are not. This difference explains why filaments grow faster at the barbed end than the pointed end. When phosphate dissociates from ADP-P i -actin through a backdoor channel, the conformation of the C terminus changes so it distorts the DNase binding loop, which allows cofilin binding, and a network of interactions among S14, H73, G74, N111, R177, and G158 rearranges to open the phosphate release site.


    Organizational Affiliation

    Department of Cell Biology, Yale University, New Haven, CT 06520-8103.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103; thomas.pollard@yale.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, alpha skeletal muscle
A, B, C, D
375Gallus gallusMutation(s): 0 
Gene Names: ACTA1 (ACTA)
Find proteins for P68139 (Gallus gallus)
Go to Gene View: ACTA1
Go to UniProtKB:  P68139
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A, B, C, D
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM026132
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM026338

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release