3MN5

Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation

• PDB DOI:  https://doi.org/10.2210/pdb3MN5/pdb

• Classification: Contractile Protein/Protein binding
• Organism(s): Oryctolagus cuniculus, Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-21 Released: 2010-06-02 
• Deposition Author(s): Ducka, A.M., Sitar, T., Popowicz, G.M., Huber, R., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation.

Ducka, A.M., Joel, P., Popowicz, G.M., Trybus, K.M., Schleicher, M., Noegel, A.A., Huber, R., Holak, T.A., Sitar, T.

(2010) Proc Natl Acad Sci U S A 107: 11757-11762

• PubMed: 20538977 
• DOI: https://doi.org/10.1073/pnas.1005347107
• Primary Citation of Related Structures:  
  3MMV, 3MN5, 3MN6, 3MN7, 3MN9


• PubMed Abstract: 
  

Three classes of proteins are known to nucleate new filaments: the Arp2/3 complex, formins, and the third group of proteins that contain ca. 25 amino acid long actin-binding Wiskott-Aldrich syndrome protein homology 2 domains, called the WH2 repeats. Crystal structures of the complexes between the actin-binding WH2 repeats of the Spire protein and actin were determined for the Spire single WH2 domain D, the double (SpirCD), triple (SpirBCD), quadruple (SpirABCD) domains, and an artificial Spire WH2 construct comprising three identical D repeats (SpirDDD). SpirCD represents the minimal functional core of Spire that can nucleate actin filaments. Packing in the crystals of the actin complexes with SpirCD, SpirBCD, SpirABCD, and SpirDDD shows the presence of two types of assemblies, "side-to-side" and "straight-longitudinal," which can serve as actin filament nuclei. The principal feature of these structures is their loose, open conformations, in which the sides of actins that normally constitute the inner interface core of a filament are flipped inside out. These Spire structures are distant from those seen in the filamentous nuclei of Arp2/3, formins, and in the F-actin filament.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, 82152 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.34 kDa 
• Atom Count: 3,418 
• Modelled Residue Count: 367 
• Deposited Residue Count: 397 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	359	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein spire	B [auth S]	38	Drosophila melanogaster	Mutation(s): 0  Gene Names: spir, p150-Spir, CG10076
UniProt
Find proteins for Q9U1K1 (Drosophila melanogaster) Explore Q9U1K1  Go to UniProtKB:  Q9U1K1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LAB	E [auth A]	LATRUNCULIN B C20 H29 N O5 S NSHPHXHGRHSMIK-JRIKCGFMSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 71.81	β = 90
c = 100.72	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Ducka, A.M., Sitar, T., Popowicz, G.M., Huber, R., Holak, T.A.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description