6W17

Structure of Dip1-activated Arp2/3 complex with nucleated actin filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.

Shaaban, M.Chowdhury, S.Nolen, B.J.

(2020) Nat Struct Mol Biol 27: 1009-1016

  • DOI: https://doi.org/10.1038/s41594-020-0481-x
  • Primary Citation of Related Structures:  
    6W17, 6W18

  • PubMed Abstract: 

    Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.


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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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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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
Protein dip1374Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: dip1SPBC24C6.10c
UniProt
Find proteins for O74771 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
I, J, K, L
377Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Phalloidin
M, N, O, P, Q
7Amanita phalloidesMutation(s): 0 
UniProt
Find proteins for P0CU63 (Amanita phalloides)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
S [auth A],
U [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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BA [auth L],
V [auth I],
X [auth J],
Z [auth K]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth K]
CA [auth L]
R [auth A]
T [auth B]
W [auth I]
AA [auth K],
CA [auth L],
R [auth A],
T [auth B],
W [auth I],
Y [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
I, J, K, L
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
ALO
Query on ALO
M, N, O, P, Q
L-PEPTIDE LINKINGC4 H9 N O3THR
G5G
Query on G5G
M, N, O, P, Q
L-PEPTIDE LINKINGC6 H13 N O4LEU
HYP
Query on HYP
M, N, O, P, Q
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.6
MODEL REFINEMENTPHENIX

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 StatesR01GM127440, R01GM092917, S10OD012272

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references