9P3D | pdb_00009p3d

cryo-EM structure of Vibrio effector VopV fragment bound to skeletal alpha F-actin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Actin isoform-specific interactions revealed by Vibrio VopV actin-binding repeats.

Kudryashova, E.Kreutzberger, M.A.B.Niedzialkowska, E.Dong, S.Kudryashov, D.S.Egelman, E.H.

(2025) Proc Natl Acad Sci U S A 122: e2523856122-e2523856122

  • DOI: https://doi.org/10.1073/pnas.2523856122
  • Primary Citation of Related Structures:  
    9P1I, 9P3D

  • PubMed Abstract: 

    Despite an evolutionary separation of over 300 Mya, there are no amino acid substitutions in certain actin isoforms from reptiles to mammals. What divergence that does exist between different actin isoforms is primarily tissue-specific, rather than species-specific. Sorting of actin isoforms into distinct cellular compartments is believed to be controlled by actin-binding proteins (ABPs), but little is known about how ABPs can differentiate between actin isoforms. We show that the actin-binding repeat (ABR) of the Vibrio parahaemolyticus effector VopV binds to cytoplasmic actin in a unique mode with a low nanomolar affinity, over a thousand times stronger than to muscle actin. Actin mutagenesis and cryo-EM reconstructions reveal that isoform-specific residues of previously unassigned function deep in the cleft between the two actin protofilament strands determine this selectivity. These results suggest a mechanism of highly selective, isoform-specific interactions between actin and its partners, and have broad implications for understanding the evolution of actin. Furthermore, our findings have implications in the pathogenesis of V. parahaemolyticus, whose invasion of intestinal epithelial cells relies on the interaction of VopV with cytoplasmic F-actin.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle372Oryctolagus cuniculusMutation(s): 0 
Gene Names: ACTA1ACTA
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vibrio VopV47Vibrio choleraeMutation(s): 0 
Gene Names: MAVP-QPI_00061
UniProt
Find proteins for A0A250E4R0 (Vibrio parahaemolyticus)
Explore A0A250E4R0 
Go to UniProtKB:  A0A250E4R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A250E4R0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
AA [auth S]
DA [auth T]
FA [auth U]
HA [auth V]
JA [auth W]
AA [auth S],
DA [auth T],
FA [auth U],
HA [auth V],
JA [auth W],
LA [auth X],
NA [auth Y],
PA [auth Z],
RA [auth a],
X [auth Q],
Y [auth R]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth S]
CA [auth T]
EA [auth U]
GA [auth V]
IA [auth W]
BA [auth S],
CA [auth T],
EA [auth U],
GA [auth V],
IA [auth W],
KA [auth X],
MA [auth Y],
OA [auth Z],
QA [auth a],
W [auth Q],
Z [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONIHRSR

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM114666
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM122510

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references