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- PDB-9p3d: cryo-EM structure of Vibrio effector VopV fragment bound to skele... -

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Basic information

Entry
Database: PDB / ID: 9p3d
Titlecryo-EM structure of Vibrio effector VopV fragment bound to skeletal alpha F-actin
Components
  • Actin, alpha skeletal muscle
  • Vibrio VopV
KeywordsSTRUCTURAL PROTEIN / T3SS / actin binding / Vibrio effector proteins / actin isoforms
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Uncharacterized protein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Vibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger, M.A. / Kudryashova, E. / Egelman, E.H. / Kudryashov, D.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM114666 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM122510 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Actin isoform-specific interactions revealed by Vibrio VopV actin-binding repeat
Authors: Kudryashova, E. / Kreutzberger, M.A.B. / Niedzialkowska, E. / Dong, S. / Egelman, E.H. / Kudryashov, D.S.
History
DepositionJun 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q: Actin, alpha skeletal muscle
R: Actin, alpha skeletal muscle
S: Actin, alpha skeletal muscle
T: Actin, alpha skeletal muscle
U: Actin, alpha skeletal muscle
V: Actin, alpha skeletal muscle
W: Actin, alpha skeletal muscle
X: Actin, alpha skeletal muscle
Y: Actin, alpha skeletal muscle
Z: Actin, alpha skeletal muscle
a: Actin, alpha skeletal muscle
c: Vibrio VopV
d: Vibrio VopV
e: Vibrio VopV
f: Vibrio VopV
g: Vibrio VopV
h: Vibrio VopV
i: Vibrio VopV
j: Vibrio VopV
k: Vibrio VopV
l: Vibrio VopV
m: Vibrio VopV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,22044
Polymers514,38422
Non-polymers5,83622
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41503.320 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide
Vibrio VopV


Mass: 5258.903 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: MAVP-QPI_00061 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A250E4R0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: VopV fragment bund to skelteal muscle F-actin / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 300 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
14IHRSR3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.66 ° / Axial rise/subunit: 27.53 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73851
Details: Helical refinement was performed in cryoSPARC. This map was then low pass filtered to 3.8 angstroms in cryoSPARC. Helical symmetry was then uniformly imposed on this map using the himpose ...Details: Helical refinement was performed in cryoSPARC. This map was then low pass filtered to 3.8 angstroms in cryoSPARC. Helical symmetry was then uniformly imposed on this map using the himpose function in IHRSR. This allowed for easier model building and interpretation of the density map.
Symmetry type: HELICAL

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