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- PDB-8vfm: Salmonella effector protein SipA decorated actin filament -

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Basic information

Entry
Database: PDB / ID: 8vfm
TitleSalmonella effector protein SipA decorated actin filament
Components
  • Actin, alpha skeletal muscle
  • Cell invasion protein SipA
KeywordsCELL INVASION / effector / SipA / actin
Function / homology
Function and homology information


Striated Muscle Contraction / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / 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 / stress fiber / skeletal muscle fiber development / 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
ADENOSINE-5'-DIPHOSPHATE / Cell invasion protein SipA / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSalmonella (bacteria)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo, E.Z. / Galan, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI055472 United States
CitationJournal: To Be Published
Title: Salmonella effector protein SipA decorated actin filament
Authors: Guo, E.Z. / Galan, J.E.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cell invasion protein SipA
A: Cell invasion protein SipA
C: Cell invasion protein SipA
I: Cell invasion protein SipA
J: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
N: Actin, alpha skeletal muscle
R: Actin, alpha skeletal muscle
S: Actin, alpha skeletal muscle
U: Actin, alpha skeletal muscle
W: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)636,65528
Polymers633,04312
Non-polymers3,61216
Water00
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
Cell invasion protein SipA / Effector protein SipA


Mass: 74040.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella (bacteria) / Gene: sipA, sspA, STM2882 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL52
#2: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Salmonella effector SipA decorated actin filamentCOMPLEX#1-#20MULTIPLE SOURCES
2Salmonella effector protein SipAORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3actinORGANELLE OR CELLULAR COMPONENT#21NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Salmonella (bacteria)590Typhimurium str. SL1344
23Gallus gallus (chicken)9031
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.2 sec. / Electron dose: 68.1384 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1SPARXparticle selection
4RELIONCTF correction
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 53.33 ° / Axial rise/subunit: 109.86 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 320109
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320109 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00928924
ELECTRON MICROSCOPYf_angle_d1.01939240
ELECTRON MICROSCOPYf_dihedral_angle_d4.70317428
ELECTRON MICROSCOPYf_chiral_restr0.0654380
ELECTRON MICROSCOPYf_plane_restr0.0075032

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