8UXX

Arp2/3 branch junction complex, BeFx state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3427Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P32390 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP32390
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2390Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9UUJ1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UUJ1 
Go to UniProtKB:  Q9UUJ1
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UniProt GroupQ9UUJ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1377Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP78774
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2317Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O14241 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupO14241
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3174Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9Y7J4 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9Y7J4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q92352 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5152Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q10316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle377Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
T [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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BA [auth N]
EA [auth O]
HA [auth P]
KA [auth Q]
NA [auth R]
BA [auth N],
EA [auth O],
HA [auth P],
KA [auth Q],
NA [auth R],
P [auth A],
V [auth H],
X [auth I],
Y [auth M]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF (Subject of Investigation/LOI)
Query on BEF

Download Ideal Coordinates CCD File 
AA [auth M]
DA [auth N]
GA [auth O]
JA [auth P]
MA [auth Q]
AA [auth M],
DA [auth N],
GA [auth O],
JA [auth P],
MA [auth Q],
PA [auth R],
R [auth A]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
CA [auth N]
FA [auth O]
IA [auth P]
LA [auth Q]
OA [auth R]
CA [auth N],
FA [auth O],
IA [auth P],
LA [auth Q],
OA [auth R],
Q [auth A],
S [auth B],
U [auth H],
W [auth I],
Z [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
H
I
J [auth M]
K [auth N]
L [auth O]
H,
I,
J [auth M],
K [auth N],
L [auth O],
M [auth P],
N [auth Q],
O [auth R]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0

Structure Validation

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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, Structure summary