6DEC | pdb_00006dec

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 (Depositor), 0.342 (DCC) 
  • R-Value Work: 
    0.275 (Depositor), 0.317 (DCC) 
  • R-Value Observed: 
    0.277 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.15252/embj.2018100005
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 553.2 kDa 
  • Atom Count: 20,563 
  • Modeled Residue Count: 4,070 
  • Deposited Residue Count: 4,887 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 3A,
I [auth H]
418Bos taurusMutation(s): 0 
UniProt
Find proteins for P61157 (Bos taurus)
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UniProt GroupP61157
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2B,
J [auth I]
394Bos taurusMutation(s): 0 
UniProt
Find proteins for A7MB62 (Bos taurus)
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UniProt GroupA7MB62
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1BC,
K [auth J]
372Bos taurusMutation(s): 0 
UniProt
Find proteins for Q58CQ2 (Bos taurus)
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UniProt GroupQ58CQ2
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2D,
L [auth K]
300Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3MHR7 (Bos taurus)
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UniProt GroupQ3MHR7
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3E,
M [auth L]
178Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T035 (Bos taurus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4
F, N
168Bos taurusMutation(s): 0 
UniProt
Find proteins for Q148J6 (Bos taurus)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5
G, O
151Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3SYX9 (Bos taurus)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
NCK-interacting protein with SH3 domainH [auth M],
P
455Homo sapiensMutation(s): 0 
Gene Names: NCKIPSDAF3P21SPIN90
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ3 (Homo sapiens)
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Go to UniProtKB:  Q9NZQ3
PHAROS:  Q9NZQ3
GTEx:  ENSG00000213672 
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UniProt GroupQ9NZQ3
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
unidentified6Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
unidentified9Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
T [auth A],
V [auth B],
X [auth H],
Z [auth I]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
S [auth A],
U [auth B],
W [auth H],
Y [auth I]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free:  0.314 (Depositor), 0.342 (DCC) 
  • R-Value Work:  0.275 (Depositor), 0.317 (DCC) 
  • R-Value Observed: 0.277 (Depositor) 
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 


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
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description