7TPT

Single-particle Cryo-EM structure of Arp2/3 complex at branched-actin junction.


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 1.1 of the entry. See complete history


Literature

Structure of Arp2/3 complex at a branched actin filament junction resolved by single-particle cryo-electron microscopy.

Ding, B.Narvaez-Ortiz, H.Y.Singh, Y.Hocky, G.M.Chowdhury, S.Nolen, B.J.

(2022) Proc Natl Acad Sci U S A 119: e2202723119-e2202723119

  • DOI: https://doi.org/10.1073/pnas.2202723119
  • Primary Citation of Related Structures:  
    7TPT

  • PubMed Abstract: 

    Arp2/3 complex nucleates branched actin filaments that provide pushing forces to drive cellular processes such as lamellipodial protrusion and endocytosis. Arp2/3 complex is intrinsically inactive, and multiple classes of nucleation promoting factors (NPFs) stimulate its nucleation activity. When activated by WASP family NPFs, the complex must bind to the side of a preexisting (mother) filament of actin to complete the nucleation process, ensuring that WASP-mediated activation creates branched rather than linear actin filaments. How actin filaments contribute to activation is currently not understood, largely due to the lack of high-resolution structures of activated Arp2/3 complex bound to the side of a filament. Here, we present the 3.9-Å cryo-electron microscopy structure of the Arp2/3 complex at a branch junction. The structure reveals contacts between Arp2/3 complex and the side of the mother actin filament that likely stimulate subunit flattening, a conformational change that allows the actin-related protein subunits in the complex (Arp2 and Arp3) to mimic filamentous actin subunits. In contrast, limited contact between the bottom half of the complex and the mother filament suggests that clamp twisting, a second major conformational change observed in the active state, is not stimulated by actin filaments, potentially explaining why actin filaments are required but insufficient to trigger nucleation during WASP-mediated activation. Along with biochemical and live-cell imaging data and molecular dynamics simulations, the structure reveals features critical for the interaction of Arp2/3 complex with actin filaments and regulated assembly of branched actin filament networks in cells.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
UniProt
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UniProt GroupP61157
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
UniProt
Find proteins for A7MB62 (Bos taurus)
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UniProt GroupA7MB62
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
UniProt
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UniProt GroupQ58CQ2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
UniProt
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UniProt GroupQ3MHR7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T035 (Bos taurus)
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UniProt GroupQ3T035
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle
H, I, J, K, L
H, I, J, K, L, M, N, O, P, Q, R, S, T, U
377Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
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UniProt GroupP68135
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Phalloidin7Amanita phalloidesMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BB [auth N]
DB [auth O]
FB [auth P]
HB [auth Q]
JB [auth R]
BB [auth N],
DB [auth O],
FB [auth P],
HB [auth Q],
JB [auth R],
LA [auth A],
LB [auth S],
NA [auth B],
NB [auth T],
OA [auth H],
PB [auth U],
RA [auth I],
TA [auth J],
VA [auth K],
XA [auth L],
ZA [auth M]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth N]
CB [auth O]
EB [auth P]
GB [auth Q]
IB [auth R]
AB [auth N],
CB [auth O],
EB [auth P],
GB [auth Q],
IB [auth R],
KA [auth A],
KB [auth S],
MA [auth B],
MB [auth T],
OB [auth U],
PA [auth H],
QA [auth I],
SA [auth J],
UA [auth K],
WA [auth L],
YA [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
H, I, J, K, L
H, I, J, K, L, M, N, O, P, Q, R, S, T, U
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
HYP
Query on HYP
AA [auth f]
BA [auth g]
CA [auth h]
DA [auth i]
EA [auth j]
AA [auth f],
BA [auth g],
CA [auth h],
DA [auth i],
EA [auth j],
FA [auth k],
GA [auth l],
HA [auth m],
IA [auth n],
JA [auth o],
V [auth a],
W [auth b],
X [auth c],
Y [auth d],
Z [auth e]
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
RECONSTRUCTIONcryoSPARCversion 2
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: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references