6DJN

Cryo-EM structure of ADP-Pi-actin filaments

  • Classification: CONTRACTILE PROTEIN
  • Organism(s): Gallus gallus
  • Mutation(s): No 

  • Deposited: 2018-05-25 Released: 2019-02-27 
  • Deposition Author(s): Chou, S.Z., Pollard, T.D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 116: 4265-4274

  • DOI: 10.1073/pnas.1807028115
  • Primary Citation of Related Structures:  
    6DJM, 6DJO, 6DJN

  • 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 i (ADP with inorganic phosphate, resolution 3.1 Å), or ADP (resolution 3.6 Å) ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleA, B, C, D375Gallus gallusMutation(s): 0 
Gene Names: ACTA1ACTA
UniProt
Find proteins for P68139 (Gallus gallus)
Explore P68139 
Go to UniProtKB:  P68139
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
A, B, C, DL-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM026132
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM026338

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence