Straight actin filament from Arp2/3 branch junction sample (ADP-BeFx)

Experimental Data Snapshot

  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Cryo-EM structures reveal how phosphate release from Arp3 weakens actin filament branches formed by Arp2/3 complex.

Chavali, S.S.Chou, S.Z.Cao, W.Pollard, T.D.De La Cruz, E.M.Sindelar, C.V.

(2024) Nat Commun 15: 2059-2059

  • DOI: https://doi.org/10.1038/s41467-024-46179-x
  • Primary Citation of Related Structures:  
    8UXW, 8UXX, 8UZ0, 8UZ1

  • PubMed Abstract: 

    Arp2/3 complex nucleates branched actin filaments for cell and organelle movements. Here we report a 2.7 Å resolution cryo-EM structure of the mature branch junction formed by S. pombe Arp2/3 complex that provides details about interactions with both mother and daughter filaments. We determine a second structure at 3.2 Å resolution with the phosphate analog BeF x bound with ADP to Arp3 and ATP bound to Arp2. In this ADP-BeF x transition state the outer domain of Arp3 is rotated 2° toward the mother filament compared with the ADP state and makes slightly broader contacts with actin in both the mother and daughter filaments. Thus, dissociation of P i from the ADP-P i transition state reduces the interactions of Arp2/3 complex with the actin filaments and may contribute to the lower mechanical stability of mature branch junctions with ADP bound to the Arps. Our structures also reveal that the mother filament in contact with Arp2/3 complex is slightly bent and twisted, consistent with the preference of Arp2/3 complex binding curved actin filaments. The small degree of twisting constrains models of actin filament mechanics.

  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208103, New Haven, CT, 06520-8103, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle372Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
Find proteins for P68139 (Gallus gallus)
Explore P68139 
Go to UniProtKB:  P68139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68139
Sequence Annotations
  • 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 
BA [auth P]
EA [auth Q]
HA [auth R]
M [auth K]
BA [auth P],
EA [auth Q],
HA [auth R],
M [auth K],
P [auth L],
S [auth M],
V [auth N],
Y [auth O]
C10 H15 N5 O10 P2
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
AA [auth O]
DA [auth P]
GA [auth Q]
JA [auth R]
L [auth J]
AA [auth O],
DA [auth P],
GA [auth Q],
JA [auth R],
L [auth J],
O [auth K],
R [auth L],
U [auth M],
X [auth N]
Be F3
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth P]
FA [auth Q]
IA [auth R]
K [auth J]
N [auth K]
CA [auth P],
FA [auth Q],
IA [auth R],
K [auth J],
N [auth K],
Q [auth L],
T [auth M],
W [auth N],
Z [auth O]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on HIC
A [auth J]
B [auth K]
C [auth L]
D [auth M]
E [auth N]
A [auth J],
B [auth K],
C [auth L],
D [auth M],
E [auth N],
F [auth O],
G [auth P],
H [auth Q],
I [auth R]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion

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 StatesR35GM136656
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM026338
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM110530

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Database references, Source and taxonomy