8E9B

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Mechanism of actin filament branch formation by Arp2/3 complex revealed by a high-resolution cryo-EM structureof the branch junction.

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

(2022) Proc Natl Acad Sci U S A 119: e2206722119-e2206722119

  • DOI: https://doi.org/10.1073/pnas.2206722119
  • Primary Citation of Related Structures:  
    8E9B

  • PubMed Abstract: 

    We reconstructed the structure of actin filament branch junctions formed by fission yeast Arp2/3 complex at 3.5 Å resolution from images collected by electron cryo-microscopy. During specimen preparation, all of the actin subunits and Arp3 hydrolyzed their bound adenosine triphosphate (ATP) and dissociated the γ-phosphate, but Arp2 retained the γ-phosphate. Binding tightly to the side of the mother filament and nucleating the daughter filament growing as a branch requires Arp2/3 complex to undergo a dramatic conformational change where two blocks of structure rotate relative to each other about 25° to align Arp2 and Arp3 as the first two subunits in the branch. During branch formation, Arp2/3 complex acquires more than 8,000 Å 2 of new buried surface, accounting for the stability of the branch. Inactive Arp2/3 complex binds only transiently to the side of an actin filament, because its conformation allows only a subset of the interactions found in the branch junction.


  • Organizational Affiliation

    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3427Schizosaccharomyces pombe 972h-Mutation(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 pombe 972h-Mutation(s): 0 
UniProt
Find proteins for Q9UUJ1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9UUJ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1377Schizosaccharomyces pombe 972h-Mutation(s): 0 
UniProt
Find proteins for P78774 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2317Schizosaccharomyces pombe 972h-Mutation(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 pombe 972h-Mutation(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 pombe 972h-Mutation(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 pombe 972h-Mutation(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 muscle375Gallus gallusMutation(s): 0 
UniProt
Find proteins for P68139 (Gallus gallus)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
S [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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AA [auth P]
CA [auth Q]
EA [auth R]
GA [auth H]
IA [auth I]
AA [auth P],
CA [auth Q],
EA [auth R],
GA [auth H],
IA [auth I],
Q [auth A],
U [auth M],
W [auth N],
Y [auth O]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth Q]
DA [auth R]
FA [auth H]
HA [auth I]
P [auth A]
BA [auth Q],
DA [auth R],
FA [auth H],
HA [auth I],
P [auth A],
R [auth B],
T [auth M],
V [auth N],
X [auth O],
Z [auth P]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
H [auth M]
I [auth N]
J [auth O]
K [auth P]
L [auth Q]
H [auth M],
I [auth N],
J [auth O],
K [auth P],
L [auth Q],
M [auth R],
N [auth H],
O [auth I]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.20.1

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 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: 2023-02-01
    Type: Initial release