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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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: 10.15252/embj.2018100005
  • Primary Citation of Related Structures:  
    6DED, 6DEC, 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 n ...

    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 3AH418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
Find proteins for P61157 (Bos taurus)
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Go to UniProtKB:  P61157
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2BI394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
Find proteins for A7MB62 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BCJ372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2DK300Bos taurusMutation(s): 0 
Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus)
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Go to UniProtKB:  Q3MHR7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3EL178Bos taurusMutation(s): 0 
Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4FN168Bos taurusMutation(s): 0 
Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5GO151Bos taurusMutation(s): 0 
Gene Names: ARPC5
Find proteins for Q3SYX9 (Bos taurus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NCK-interacting protein with SH3 domainMP455Homo sapiensMutation(s): 0 
Gene Names: NCKIPSDAF3P21SPIN90
Find proteins for Q9NZQ3 (Homo sapiens)
Explore Q9NZQ3 
Go to UniProtKB:  Q9NZQ3
NIH Common Fund Data Resources
PHAROS  Q9NZQ3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
unidentifiedQ6Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
unidentifiedR9Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
A, B, H, I
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-11 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Nolen, B.J., Luan, Q.

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

Revision History 

  • 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