2GWJ | pdb_00002gwj

SpvB ADP-ribosylated actin: hexagonal crystal form

• PDB DOI: https://doi.org/10.2210/pdb2GWJ/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): Yes 


• Deposited: 2006-05-04 Released: 2006-08-29 
• Deposition Author(s): Stebbins, C.E., Margarit, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.184 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

A steric antagonism of actin polymerization by a salmonella virulence protein.

Margarit, S.M., Davidson, W., Frego, L., Stebbins, C.E.

(2006) Structure 14: 1219-1229

• PubMed: 16905096 
• DOI: https://doi.org/10.1016/j.str.2006.05.022
• Primary Citation Related Structures: 
  2GWJ, 2GWK, 2GWL, 2GWM


• PubMed Abstract: 
  

  Salmonella spp. require the ADP-ribosyltransferase activity of the SpvB protein for intracellular growth and systemic virulence. SpvB covalently modifies actin, causing cytoskeletal disruption and apoptosis. We report here the crystal structure of the catalytic domain of SpvB, and we show by mass spectrometric analysis that SpvB modifies actin at Arg177, inhibiting its ATPase activity. We also describe two crystal structures of SpvB-modified, polymerization-deficient actin. These structures reveal that ADP-ribosylation does not lead to dramatic conformational changes in actin, suggesting a model in which this large family of toxins inhibits actin polymerization primarily through steric disruption of intrafilament contacts.

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Organizational Affiliation: 
• Laboratory of Structural Microbiology, Rockefeller University, New York, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.93 kDa 
• Atom Count: 3,271 
• Modeled Residue Count: 360 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	371	Oryctolagus cuniculus	Mutation(s): 1  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.184 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.361	α = 90
b = 96.361	β = 90
c = 97.41	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Stebbins, C.E., Margarit, S.M.

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary