6DEC

Crystal structure of Bos taurus Arp2/3 complex binding with C-terminus of Homo sapiens SPIN90

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 

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Literature

Structure of the nucleation-promoting factor SPIN90 bound to the actin filament nucleator Arp2/3 complex.

Luan, Q., Liu, S.L., Helgeson, L.A., Nolen, B.J.

(2018) EMBO J 37

  • DOI: https://doi.org/10.15252/embj.2018100005
  • Primary Citation of Related Structures:  
    6DEC, 6DED, 6DEE

  • PubMed Abstract: 

    • Unlike the WASP family of Arp2/3 complex activators, WISH/DIP/SPIN90 (WDS) family proteins activate actin filament nucleation by the Arp2/3 complex without the need for a preformed actin filament. This allows WDS proteins to initiate branched actin network assembly by providing seed filaments that activate WASP-bound Arp2/3 complex ...

    Unlike the WASP family of Arp2/3 complex activators, WISH/DIP/SPIN90 (WDS) family proteins activate actin filament nucleation by the Arp2/3 complex without the need for a preformed actin filament. This allows WDS proteins to initiate branched actin network assembly by providing seed filaments that activate WASP-bound Arp2/3 complex. Despite their important role in actin network initiation, it is unclear how WDS proteins drive the activating steps that require both WASP and pre-existing actin filaments during WASP-mediated nucleation. Here, we show that SPIN90 folds into an armadillo repeat domain that binds a surface of Arp2/3 complex distinct from the two WASP sites, straddling a hinge point that may stimulate movement of the Arp2 subunit into the activated short-pitch conformation. SPIN90 binds a surface on Arp2/3 complex that overlaps with actin filament binding, explaining how it could stimulate the same structural rearrangements in the complex as pre-existing actin filaments. By revealing how WDS proteins activate the Arp2/3 complex, these data provide a molecular foundation to understand initiation of dendritic actin networks and regulation of Arp2/3 complex by its activators.

    Organizational Affiliation: 

    Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA bnolen@uoregon.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 3A,
I [auth H]		418Bos taurusMutation(s): 0 
Gene Names: ACTR3, ARP3
UniProt
Find proteins for P61157 (Bos taurus)
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UniProt GroupP61157
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2B,
J [auth I]		394Bos taurusMutation(s): 0 
Gene Names: ACTR2, ARP2
UniProt
Find proteins for A7MB62 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BC,
K [auth J]		372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2D,
L [auth K]		300Bos taurusMutation(s): 0 
Gene Names: ARPC2
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3E,
M [auth L]		178Bos taurusMutation(s): 0 
Gene Names: ARPC3
UniProt
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4
F, N
168Bos taurusMutation(s): 0 
Gene Names: ARPC4
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5
G, O
151Bos taurusMutation(s): 0 
Gene Names: ARPC5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NCK-interacting protein with SH3 domainH [auth M],
P		455Homo sapiensMutation(s): 0 
Gene Names: NCKIPSD, AF3P21, SPIN90
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ3 (Homo sapiens)
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PHAROS:  Q9NZQ3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
unidentified6Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
unidentified9Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.277 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.84α = 90
b = 197.381β = 90
c = 202.067γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesR01GM092917

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence