8VFM | pdb_00008vfm

Salmonella effector protein SipA decorated actin filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization.

Guo, E.Chou, S.Z.Lara-Tejero, M.Galan, J.E.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.12.21.572903
  • Primary Citation of Related Structures:  
    8VFM

  • PubMed Abstract: 

    The bacterial pathogen Salmonella spp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion and promotes intestinal inflammation. The mechanisms by which this effector carries out these functions are incompletely understood although SipA's ability to modulate actin dynamics is central to some of these activities. Here we report the cryo-EM structure of SipA bound to filamentous actin. We show that this effector stabilizes actin filaments through unique interactions of its carboxy terminal domain with four actin subunits. Furthermore, our structure-function studies revealed that SipA's actin-binding activity is independent from its ability to stimulate intestinal inflammation. Overall, these studies illuminate critical aspects of Salmonella pathogenesis, and provide unique insight into the mechanisms by which a bacterial effector modulates actin dynamics.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell invasion protein SipAA [auth B],
B [auth A],
C,
D [auth I]
685SalmonellaMutation(s): 0 
Gene Names: sipAsspASTM2882
UniProt
Find proteins for P0CL52 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0CL52 
Go to UniProtKB:  P0CL52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CL52
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle377Gallus gallusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus)
Explore P68139 
Go to UniProtKB:  P68139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68139
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth W]
N [auth J]
P [auth L]
R [auth M]
T [auth N]
BA [auth W],
N [auth J],
P [auth L],
R [auth M],
T [auth N],
V [auth R],
X [auth S],
Z [auth U]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth W]
M [auth J]
O [auth L]
Q [auth M]
S [auth N]
AA [auth W],
M [auth J],
O [auth L],
Q [auth M],
S [auth N],
U [auth R],
W [auth S],
Y [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
E [auth J]
F [auth L]
G [auth M]
H [auth N]
I [auth R]
E [auth J],
F [auth L],
G [auth M],
H [auth N],
I [auth R],
J [auth S],
K [auth U],
L [auth W]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI055472

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection
  • Version 1.2: 2025-07-23
    Changes: Data collection, Database references