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- EMDB-71239: cryo-EM structure of Vibrio effector VopV fragment bound to skele... -

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Basic information

Entry
Database: EMDB / ID: EMD-71239
Titlecryo-EM structure of Vibrio effector VopV fragment bound to skeletal alpha F-actin
Map dataTo 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.
Sample
  • Complex: VopV fragment bund to skelteal muscle F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Vibrio VopV
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: water
KeywordsT3SS / actin binding / Vibrio effector proteins / actin isoforms / STRUCTURAL PROTEIN
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
Uncharacterized protein / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Vibrio cholerae (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger MA / Kudryashova E / Egelman EH / Kudryashov DS
Funding support United States, 2 items
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 MAB / Niedzialkowska E / Dong S / Egelman EH / Kudryashov DS
History
DepositionJun 13, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71239.png

Downloads & links

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Map

FileDownload / File: emd_71239.map.gz / Format: CCP4 / Size: 200 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTo 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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.20643026 - 0.46915033
Average (Standard dev.)0.0024910704 (±0.02100007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-256
Dimensions320320512
Spacing320320512
CellA: 265.6 Å / B: 265.6 Å / C: 424.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71239_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryoSPARC map from which primary map was generated...

Fileemd_71239_additional_1.map
AnnotationcryoSPARC map from which primary map was generated using IHRSR's himpose.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC half map A

Fileemd_71239_half_map_1.map
AnnotationcryoSPARC half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoSPARC half map B

Fileemd_71239_half_map_2.map
AnnotationcryoSPARC half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VopV fragment bund to skelteal muscle F-actin

EntireName: VopV fragment bund to skelteal muscle F-actin
Components
  • Complex: VopV fragment bund to skelteal muscle F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Vibrio VopV
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: water

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Supramolecule #1: VopV fragment bund to skelteal muscle F-actin

SupramoleculeName: VopV fragment bund to skelteal muscle F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.50332 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
SequenceString: ETTALVCDNG SGLVKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN V PIYEGYAL ...String:
ETTALVCDNG SGLVKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN V PIYEGYAL PHAIMRLDLA GRDLTDYLMK ILTERGYSFV TTAEREIVRD IKEKLCYVAL DFENEMATAA SSSSLEKSYE LP DGQVITI GNERFRCPET LFQPSFIGME SAGIHETTYN SIMKCDIDIR KDLYANNVMS GGTTMYPGIA DRMQKEITAL APS TMKIKI IAPPERKYSV WIGGSILASL STFQQMWITK QEYDEAGPSI VHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Vibrio VopV

MacromoleculeName: Vibrio VopV / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 5.258903 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
KKWPEVKIPA RIITTSGNAS VDGNPGYRPT RVDSNGETMG YEMRDRV

UniProtKB: Uncharacterized protein

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 11 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 11 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 300.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.53 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.66 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, IHRSR)
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.
Number images used: 73851
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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