6YW7

Cryo-EM structure of the ARP2/3 1A5C isoform complex.

• PDB DOI:  https://doi.org/10.2210/pdb6YW7/pdb
• EM Map EMD-10960: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-04-29 Released: 2020-07-22 
• Deposition Author(s): von Loeffelholz, O., Moores, C., Purkiss, A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM of human Arp2/3 complexes provides structural insights into actin nucleation modulation by ARPC5 isoforms.

von Loeffelholz, O., Purkiss, A., Cao, L., Kjaer, S., Kogata, N., Romet-Lemonne, G., Way, M., Moores, C.A.

(2020) Biol Open 9

• PubMed: 32661131 
• DOI: https://doi.org/10.1242/bio.054304
• Primary Citation of Related Structures:  
  6YW6, 6YW7


• PubMed Abstract: 
  

The Arp2/3 complex regulates many cellular processes by stimulating formation of branched actin filament networks. Because three of its seven subunits exist as two different isoforms, mammals produce a family of Arp2/3 complexes with different properties that may be suited to different physiological contexts. To shed light on how isoform diversification affects Arp2/3 function, we determined a 4.2 Å resolution cryo-EM structure of the most active human Arp2/3 complex containing ARPC1B and ARPC5L, and compared it with the structure of the least active ARPC1A-ARPC5-containing complex. The architecture of each isoform-specific Arp2/3 complex is the same. Strikingly, however, the N-terminal half of ARPC5L is partially disordered compared to ARPC5, suggesting that this region of ARPC5/ARPC5L is an important determinant of complex activity. Confirming this idea, the nucleation activity of Arp2/3 complexes containing hybrid ARPC5/ARPC5L subunits is higher when the ARPC5L N-terminus is present, thereby providing insight into activity differences between the different Arp2/3 complexes.

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Organizational Affiliation: 

Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A1B1C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A2B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 225.88 kDa 
• Atom Count: 5,426 
• Modelled Residue Count: 1,788 
• Deposited Residue Count: 1,979 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 3	A	418	Homo sapiens	Mutation(s): 0  Gene Names: ACTR3, ARP3
UniProt & NIH Common Fund Data Resources
Find proteins for P61158 (Homo sapiens) Explore P61158  Go to UniProtKB:  P61158
PHAROS:  P61158

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 2	B [auth D]	300	Homo sapiens	Mutation(s): 0  Gene Names: ARPC2, ARC34, PRO2446
UniProt & NIH Common Fund Data Resources
Find proteins for O15144 (Homo sapiens) Explore O15144  Go to UniProtKB:  O15144
PHAROS:  O15144

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 3	C [auth E]	178	Homo sapiens	Mutation(s): 0  Gene Names: ARPC3, ARC21
UniProt & NIH Common Fund Data Resources
Find proteins for O15145 (Homo sapiens) Explore O15145  Go to UniProtKB:  O15145
PHAROS:  O15145

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2	D [auth B]	394	Homo sapiens	Mutation(s): 0  Gene Names: ACTR2, ARP2
UniProt & NIH Common Fund Data Resources
Find proteins for P61160 (Homo sapiens) Explore P61160  Go to UniProtKB:  P61160
PHAROS:  P61160

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 4	E [auth F]	168	Homo sapiens	Mutation(s): 0  Gene Names: ARPC4, ARC20
UniProt & NIH Common Fund Data Resources
Find proteins for P59998 (Homo sapiens) Explore P59998  Go to UniProtKB:  P59998
PHAROS:  P59998

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 5	F [auth G]	151	Homo sapiens	Mutation(s): 0  Gene Names: ARPC5, ARC16
UniProt & NIH Common Fund Data Resources
Find proteins for O15511 (Homo sapiens) Explore O15511  Go to UniProtKB:  O15511
PHAROS:  O15511

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin-related protein 2/3 complex subunit 1A	G [auth C]	370	Homo sapiens	Mutation(s): 0  Gene Names: ARPC1A, SOP2L
UniProt & NIH Common Fund Data Resources
Find proteins for Q92747 (Homo sapiens) Explore Q92747  Go to UniProtKB:  Q92747
PHAROS:  Q92747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	H [auth A], I [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): von Loeffelholz, O., Moores, C., Purkiss, A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L00190X/1

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references