6UHC

CryoEM structure of human Arp2/3 complex with bound NPFs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism.

Zimmet, A.Van Eeuwen, T.Boczkowska, M.Rebowski, G.Murakami, K.Dominguez, R.

(2020) Sci Adv 6: eaaz7651-eaaz7651

  • DOI: 10.1126/sciadv.aaz7651
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 complex durin ...

    Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 complex during activation, but the order, specific interactions, and contribution of each NPF to activation are unresolved. Here, we report the cryo-electron microscopy structure of recombinantly expressed human Arp2/3 complex with two WASP family NPFs bound and address the mechanism of activation. A cross-linking assay that captures the transition of the Arps into the activated filament-like conformation shows that actin binding to NPFs favors this transition. Actin-NPF binding to Arp2 precedes binding to Arp3 and is sufficient to promote the filament-like conformation but not activation. Structure-guided mutagenesis of the NPF-binding sites reveals their distinct roles in activation and shows that, contrary to budding yeast Arp2/3 complex, NPF-mediated delivery of actin at the barbed end of both Arps is required for activation of human Arp2/3 complex.


    Organizational Affiliation

    Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 3A418Homo sapiensMutation(s): 0 
Gene Names: ACTR3ARP3
Find proteins for P61158 (Homo sapiens)
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Go to UniProtKB:  P61158
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PHAROS  P61158
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2B394Homo sapiensMutation(s): 0 
Gene Names: ACTR2ARP2
Find proteins for P61160 (Homo sapiens)
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PHAROS  P61160
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 1BC372Homo sapiensMutation(s): 0 
Gene Names: ARPC1BARC41
Find proteins for O15143 (Homo sapiens)
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PHAROS  O15143
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 2D300Homo sapiensMutation(s): 0 
Gene Names: ARPC2ARC34PRO2446
Find proteins for O15144 (Homo sapiens)
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PHAROS  O15144
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 3E203Homo sapiensMutation(s): 0 
Gene Names: ARPC3ARC21
Find proteins for O15145 (Homo sapiens)
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PHAROS  O15145
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 4F168Homo sapiensMutation(s): 0 
Gene Names: ARPC4ARC20
Find proteins for P59998 (Homo sapiens)
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PHAROS  P59998
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 5G151Homo sapiensMutation(s): 0 
Gene Names: ARPC5ARC16
Find proteins for O15511 (Homo sapiens)
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PHAROS  O15511
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Neural Wiskott-Aldrich syndrome proteinH, I501Mus musculusMutation(s): 0 
Gene Names: Wasl
Find proteins for Q91YD9 (Mus musculus)
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01-GM07391
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008275
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesF31-HL146077

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release