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- PDB-9p1i: Atomic structure of vibrio effector fragment VopV bound to Beta-c... -

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Basic information

Entry
Database: PDB / ID: 9p1i
TitleAtomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin
Components
  • Actin, cytoplasmic 1
  • VopV
KeywordsSTRUCTURAL PROTEIN / actin / Vibrio / effector proteins / T3SS / cryo-EM / actin isoforms
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions ...positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Gap junction degradation / Folding of actin by CCT/TriC / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / Tat protein binding / postsynaptic actin cytoskeleton / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / apical junction complex / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / kinesin binding / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / adherens junction / actin filament / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / kinetochore / DNA Damage Recognition in GG-NER / structural constituent of cytoskeleton / B-WICH complex positively regulates rRNA expression / VEGFA-VEGFR2 Pathway / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / platelet aggregation / Schaffer collateral - CA1 synapse / tau protein binding / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / UCH proteinases / nucleosome / actin cytoskeleton / lamellipodium / presynapse / Clathrin-mediated endocytosis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production
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, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio parahaemolyticus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 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)R35 GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM114666 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Actin isoform-specific interactions revealed by VopV actin-binding repeats.
Authors: Elena Kudryashova / Mark A B Kreutzberger / Ewa Niedzialkowska / Songyu Dong / Dmitri S Kudryashov / Edward H Egelman /
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 ...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 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 , whose invasion of intestinal epithelial cells relies on the interaction of VopV with cytoplasmic F-actin.
History
DepositionJun 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Actin, cytoplasmic 1
R: Actin, cytoplasmic 1
S: Actin, cytoplasmic 1
T: Actin, cytoplasmic 1
U: Actin, cytoplasmic 1
V: Actin, cytoplasmic 1
W: Actin, cytoplasmic 1
X: Actin, cytoplasmic 1
Y: Actin, cytoplasmic 1
Z: Actin, cytoplasmic 1
a: Actin, cytoplasmic 1
b: Actin, cytoplasmic 1
c: VopV
d: VopV
e: VopV
f: VopV
g: VopV
h: VopV
i: VopV
j: VopV
k: VopV
l: VopV
m: VopV
n: VopV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,440,17948
Polymers3,433,81324
Non-polymers6,36624
Water21612
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, cytoplasmic 1 / Beta-actin


Mass: 41795.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Komagataella pastoris (fungus)
References: UniProt: P60709, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
VopV


Mass: 244355.438 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (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.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 12 / 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.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: F-actin (75/25 Beta/Gamma) with bound VopV / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)
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: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.51particle selection
13cryoSPARC4.513D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -167 ° / Axial rise/subunit: 27.52 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140672
Details: To better reflect the helical symmetry and reliably build a multi-subunit model the original cryoSPARC volume was input into IHRSR's himpose to generate an extended helical volume.
Symmetry type: HELICAL

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