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- EMDB-43188: Salmonella effector protein SipA decorated actin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-43188
TitleSalmonella effector protein SipA decorated actin filament
Map dataEM map
Sample
  • Complex: Salmonella effector SipA decorated actin filament
    • Organelle or cellular component: Salmonella effector protein SipA
      • Protein or peptide: Cell invasion protein SipA
    • Organelle or cellular component: actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordseffector / cell invasion / SipA / actin
Function / homology
Function and homology information


Striated Muscle Contraction / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / actin binding / hydrolase activity ...Striated Muscle Contraction / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / actin binding / hydrolase activity / extracellular region / ATP binding
Similarity search - Function
Salmonella invasion protein A, C-terminal actin-binding domain superfamily / : / Salmonella Invasion protein A, C-terminal actin binding domain / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...Salmonella invasion protein A, C-terminal actin-binding domain superfamily / : / Salmonella Invasion protein A, C-terminal actin binding domain / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / 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
Cell invasion protein SipA / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSalmonella (bacteria) / Gallus gallus (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo EZ / Galan JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI055472 United States
CitationJournal: bioRxiv / Year: 2024
Title: Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization.
Authors: Emily Guo / Steven Z Chou / Maria Lara-Tejero / Jorge E Galan
Abstract: The bacterial pathogen Salmonella spp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion ...The bacterial pathogen Salmonella spp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion and promotes intestinal inflammation. The mechanisms by which this effector carries out these functions are incompletely understood although SipA's ability to modulate actin dynamics is central to some of these activities. Here we report the cryo-EM structure of SipA bound to filamentous actin. We show that this effector stabilizes actin filaments through unique interactions of its carboxy terminal domain with four actin subunits. Furthermore, our structure-function studies revealed that SipA's actin-binding activity is independent from its ability to stimulate intestinal inflammation. Overall, these studies illuminate critical aspects of Salmonella pathogenesis, and provide unique insight into the mechanisms by which a bacterial effector modulates actin dynamics.
History
DepositionDec 21, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43188.png

Downloads & links

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Map

FileDownload / File: emd_43188.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å		1.07 Å/pix.
x 320 pix.
= 341.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0434
Minimum - Maximum-0.06786636 - 1.9589043
Average (Standard dev.)0.002500171 (±0.037056796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 341.75998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM map

Fileemd_43188_half_map_1.map
AnnotationEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_43188_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Salmonella effector SipA decorated actin filament

EntireName: Salmonella effector SipA decorated actin filament
Components
  • Complex: Salmonella effector SipA decorated actin filament
    • Organelle or cellular component: Salmonella effector protein SipA
      • Protein or peptide: Cell invasion protein SipA
    • Organelle or cellular component: actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Salmonella effector SipA decorated actin filament

SupramoleculeName: Salmonella effector SipA decorated actin filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Salmonella effector protein SipA

SupramoleculeName: Salmonella effector protein SipA / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Salmonella (bacteria) / Strain: Typhimurium str. SL1344

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Supramolecule #3: actin

SupramoleculeName: actin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Cell invasion protein SipA

MacromoleculeName: Cell invasion protein SipA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella (bacteria)
Molecular weightTheoretical: 74.040781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVTSVRTQPP VIMPGMQTEI KTQATNLAAN LSAVRESATA TLSGEIKGPQ LEDFPALIKQ ASLDALFKCG KDAEALKEVF TNSNNVAGK KAIMEFAGLF RSALNATSDS PEAKTLLMKV GAEYTAQIIK DGLKEKSAFG PWLPETKKAE AKLENLEKQL L DIIKNNTG ...String:
MVTSVRTQPP VIMPGMQTEI KTQATNLAAN LSAVRESATA TLSGEIKGPQ LEDFPALIKQ ASLDALFKCG KDAEALKEVF TNSNNVAGK KAIMEFAGLF RSALNATSDS PEAKTLLMKV GAEYTAQIIK DGLKEKSAFG PWLPETKKAE AKLENLEKQL L DIIKNNTG GELSKLSTNL VMQEVMPYIA SCIEHNFGCT LDPLTRSNLT HLVDKAAAKA VEALDMCHQK LTQEQGTSVG RE ARHLEMQ TLIPLLLRNV FAQIPADKLP DPKIPEPAAG PVPDGGKKAE PTGINININI DSSNHSVDNS KHINNSRSHV DNS QRHIDN SNHDNSRKTI DNSRTFIDNS QRNGESHHST NSSNVSHSHS RVDSTTHQTE TAHSASTGAI DHGIAGKIDV TAHA TAEAV TNASSESKDG KVVTSEKGTT GETTSFDEVD GVTSKSIIGK PVQATVHGVD DNKQQSQTAE IVNVKPLASQ LAGVE NVKT DTLQSDTTVI TGNKAGTTDN DNSQTDKTGP FSGLKFKQNS FLSTVPSVTN MHSMHFDARE TFLGVIRKAL EPDTST PFP VRRAFDGLRA EILPNDTIKS AALKAQCSDI DKHPELKAKM ETLKEVITHH PQKEKLAEIA LQFAREAGLT RLKGETD YV LSNVLDGLIG DGSWRAGPAY ESYLNKPGVD RVITTVDGLH MQR

UniProtKB: Cell invasion protein SipA

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.2 sec. / Average electron dose: 68.1384 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 109.86 Å
Applied symmetry - Helical parameters - Δ&Phi: 53.33 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320109
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 320109 / Software - Name: SPARX
Startup modelType of model: EMDB MAP
EMDB ID:

7937

Final angle assignmentType: MAXIMUM LIKELIHOOD

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