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- EMDB-71108: Atomic structure of vibrio effector fragment VopV bound to Beta-c... -

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Basic information

Entry
Database: EMDB / ID: EMD-71108
TitleAtomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin
Map dataMap with helical symmetry imposed over longer distance
Sample
  • Complex: F-actin (75/25 Beta/Gamma) with bound VopV
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: VopV
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: water
Keywordsactin / Vibrio / effector proteins / T3SS / cryo-EM / actin isoforms / STRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / GBAF complex / Folding of actin by CCT/TriC / protein localization to adherens junction / regulation of G0 to G1 transition / 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 outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / 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 / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / 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 / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / adherens junction / 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 / DNA Damage Recognition in GG-NER / Regulation of actin dynamics for phagocytic cup formation / kinetochore / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / VEGFA-VEGFR2 Pathway / 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 / UCH proteinases / Signaling by BRAF and RAF1 fusions / nucleosome / presynapse / lamellipodium / actin cytoskeleton / 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
Uncharacterized protein / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 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)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.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 10, 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_71108.png

Downloads & links

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Map

FileDownload / File: emd_71108.map.gz / Format: CCP4 / Size: 200 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap with helical symmetry imposed over longer distance
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: 0.307
Minimum - Maximum-0.6972688 - 1.191848
Average (Standard dev.)0.0020643503 (±0.045403033)
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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Additional map: #1

Fileemd_71108_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71108_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71108_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-actin (75/25 Beta/Gamma) with bound VopV

EntireName: F-actin (75/25 Beta/Gamma) with bound VopV
Components
  • Complex: F-actin (75/25 Beta/Gamma) with bound VopV
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: VopV
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: water

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Supramolecule #1: F-actin (75/25 Beta/Gamma) with bound VopV

SupramoleculeName: F-actin (75/25 Beta/Gamma) with bound VopV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)

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Macromolecule #1: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.79568 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: VopV

MacromoleculeName: VopV / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)
Molecular weightTheoretical: 244.355438 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MINSLNIQNT GSISELGQSP NLTINSAPAP SVLPRSEALA NSNDVLPSAV TAQDSCFEQG EEKLTENNNV NKPAKNKKVN CKSNKYNNK TKAKTHLAAI AGATTLGAVL APFTGGLSLL PTAFVVLFGN ASALAMYGGS EFFLGQNAIN KEEVPKDKLK E KETPETAL ...String:
MINSLNIQNT GSISELGQSP NLTINSAPAP SVLPRSEALA NSNDVLPSAV TAQDSCFEQG EEKLTENNNV NKPAKNKKVN CKSNKYNNK TKAKTHLAAI AGATTLGAVL APFTGGLSLL PTAFVVLFGN ASALAMYGGS EFFLGQNAIN KEEVPKDKLK E KETPETAL KRTPERPIFP RYLERRTHFD EVDGLKRNGP DSFNVTNNYY SPTFNINVGD YFFNNQTNNR DESKAEDKPF AE SAAQSDV SSQTTTLFDE AIQNMGQLQV VDVSEISPDT LFSEVTDHAT NIGTEDTVDN LLGALESCHL QSGQAKLVKV TLE GGLQAY LGGISDDTAD ALPPVVTENV TSSPVKKWPE VKIPARIITT SGNASVDGNP GYRPTRVDSN GETMGYEMRD RVSS SSTPS QSTATSSKGS VNTERSATQT GTPAQADSTK GVEPNVSTPE QKPSADASNG EPTSVQGKTS EGIDSGVGTP ESTPS MDAA TGEPNTADDK HAVGESTPTH ESGESVASVE SEPASSGPAK RWPEVKTPAR VITSAGNASV DGNPGYRPTR VDSNGE TMG YEMRDRVSSS STPSPSTAPS SKGSVNAEGN APQTGTPAQA GSSKGVEPNV ATPEQKPSAD VSSGEPTSAQ GNASEGI DS GVATPEQKPS ADAFSGEPTS AQGNASEGID AGVATPEQKP SMGASSGEPT SAQGNASEGT DSGVGTPEST PSVDAATG E PNTADDKNAV GESTPTHESG ESVPSVESEQ ASSGPAKRWP EVKTPARVIT SAGNASIDGN PGYRPTRVDS NGETMGYEM RDRVPASSTP SASTGPSSKG SVNAEGNAPQ TGTPAQAGSS KGVEPNVATP EQKPSADASS GEPTAAQGNA SEGIDSGVGT PESTPSVDA ATGEPNTADD KNAVGESTPT HESGESVPSV ESEQASSGPA KRWPEVKTPA RVITSAGNAS IDGNPGYRPT R VDSNGETM GYEMRDRVPA SSTPSPSSAP SSNGSVNAEG NAPQTGTPTQ AGSSNVEPSV ATPEQKPSAD ASSGEPISTQ GN APESIDS GVATPEQKPS AEASSGEPTS AQGNASEGID SGVDTPESTP SVDAATGEPN TADNKNAAGE STPSVEPEQA PSG PAKRWP EVKTPARVIT SAGNASIDGN PGYRPTRVDS NGETMGYEMR DRVPASSTPS ASTAPSSKGS VNAEGNAPQT GTPA QAGSA NVEPKVATPE QKTSADVSRG EPTLTQGNAP EGIDSGVATP EQKPSVSGST DEPTLAQGNA PEGIDAGVST PESTP SVDA ATGEPNTADD KNAAGESIPT LAEGATPTHE SGESVPSVEP EQTSSGPAKR WPEVKTPARV ITSAGNASID GNPGYR PTR VDSNGETMGY EMRDRVPASS TPSASTAASS KGSVNAEGNA PQTGTPAQAG SSNVEPSVAT PEQKPSADAF SGEPTSA QG NAPEGIDAGV STPESTPSVD AATGEPNTAD DKNAAGESIP TLAEGATPTH ESGESVPSVE PEQTSSGPAK RWPEVKTP A RVITSAGNAS IDGNPGYRPT RVDSNGETMG YEMRDRVPAS STPSASTAAS SKGSVNAEGN APQTGTPAQA GSSNVEPSV ATPEQKPSVS GSTDEPTLAQ GNASEGIDAG VSTPESTPSV DAATGEPNTA DNKNAAGESI PTLAEGATPT HESGESVPSV EPEQTSSGP AKRWPEVKTP ARVITSAGNA SIDGNPGYRP TRVDSNGETM GYEMRDRVPA SSTPSASTAA SSKGSVNAEG N APQTGTPA QAGSSNVEPS VATPEQKPSA DAFSGEPTSA QGNAPEGIDA GVSTPESTPS VDAATGEPNT ADDKNAAGES IP TLAEGAT PTHESGESVP SVEPEQTSSG PAKRWPEVKT PARVITSAGN ASIDGNPGYR PTRVDSNGET MGYEMRDRVP ASS TPSAST AASSKGSVNA EGNAPQTGTP AQAGSSNVEP SVATPEQKPS VSGSTDEPTL AQGNASEGID AGVSTPESTP SVDA ATGEP NTADNKNAVG ESSPTHESGE SVPSVEPEQT SSGPAKRWPE VKTPARVITS AGNASIDGNP GYRPTRVDSN GETMG YEMR DRVPASSTPS ASTAASSKGS VNAEGNAPQT GTPAQAGSSN VEPSVATPEQ KPSADAFSGE PTSAQGNAPE GIDAGV STP ESTPSVDEVN HLATSQEKEV SESSFTHRSE IKFHVNAEID TDINPLGERF TSTLKVNLGS GQASIQTQAS DSFVDWQ SA QVEDGIEFKE AVLVTEDVKD EILWATGELN DGPELRFAKK IDNSSAQNFE SGLDNQRTAS SGVARNEGST KEVVGSVS G KKWKVNMPAP VLTTQGMMSG HARNYTQGIL NNIRDLNTTR KEYETTLVSG LVGSNSSVSI WAHSERSMVV PVANSSNFK MM

UniProtKB: Uncharacterized protein

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / 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: 12 / 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: 12 / 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 27.52 Å
Applied symmetry - Helical parameters - Δ&Phi: -167 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.51)
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.
Number images used: 140672
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

27114

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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