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: 4.6 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China.,Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 3
A, H
418Bos taurusMutation(s): 0 
Gene Names: ACTR3 (ARP3)
Find proteins for P61157 (Bos taurus)
Go to Gene View: ACTR3
Go to UniProtKB:  P61157
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2
B, I
394Bos taurusMutation(s): 0 
Gene Names: ACTR2 (ARP2)
Find proteins for A7MB62 (Bos taurus)
Go to Gene View: ACTR2
Go to UniProtKB:  A7MB62
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 1B
C, J
372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus)
Go to Gene View: ARPC1B
Go to UniProtKB:  Q58CQ2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 2
D, K
300Bos taurusMutation(s): 0 
Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus)
Go to Gene View: ARPC2
Go to UniProtKB:  Q3MHR7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 3
E, L
178Bos taurusMutation(s): 0 
Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus)
Go to Gene View: ARPC3
Go to UniProtKB:  Q3T035
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 4
F, N
168Bos taurusMutation(s): 0 
Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus)
Go to Gene View: ARPC4
Go to UniProtKB:  Q148J6
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 5
G, O
151Bos taurusMutation(s): 0 
Gene Names: ARPC5
Find proteins for Q3SYX9 (Bos taurus)
Go to Gene View: ARPC5
Go to UniProtKB:  Q3SYX9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NCK-interacting protein with SH3 domain
M, P
455Homo sapiensMutation(s): 0 
Gene Names: NCKIPSD (AF3P21, SPIN90)
Find proteins for Q9NZQ3 (Homo sapiens)
Go to Gene View: NCKIPSD
Go to UniProtKB:  Q9NZQ3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
unidentified
Q
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
unidentified
R
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
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 SDF File 
Download CCD File 
A, B, H, I
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
Q, R
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.6 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.275 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 179.840α = 90.00
b = 197.381β = 90.00
c = 202.067γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 ServicesUnited StatesR01GM092917

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references