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- PDB-8vaa: Actin-binding domain of Legionella pneumophila effector LFAT1 (lp... -

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Basic information

Entry
Database: PDB / ID: 8vaa
TitleActin-binding domain of Legionella pneumophila effector LFAT1 (lpg1387) bound to F-actin
Components
  • Actin, alpha skeletal muscle
  • F-actin-binding Coiled-Coil domain of LFAT1
KeywordsTOXIN / Complex / F-actin binding domain / lysine fatty-acyltransferase / coiled-coil
Function / homology
Function and homology information


Striated Muscle Contraction / Formation of the dystrophin-glycoprotein complex (DGC) / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...Striated Muscle Contraction / Formation of the dystrophin-glycoprotein complex (DGC) / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / lamellipodium / cell body / hydrolase activity / positive regulation of gene expression / ATP binding / cytosol / 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
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZeng, W. / Mao, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM135379-01 United States
CitationJournal: Elife / Year: 2025
Title: Cryo-EM structure revealed a novel F-actin binding motif in a Legionella pneumophila lysine fatty-acyltransferase
Authors: Zeng, W.W. / Komaniecki, G. / Liu, J. / Lin, H. / Mao, Y.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: F-actin-binding Coiled-Coil domain of LFAT1
L: F-actin-binding Coiled-Coil domain of LFAT1
M: F-actin-binding Coiled-Coil domain of LFAT1
N: F-actin-binding Coiled-Coil domain of LFAT1
O: F-actin-binding Coiled-Coil domain of LFAT1
P: F-actin-binding Coiled-Coil domain of LFAT1
Q: F-actin-binding Coiled-Coil domain of LFAT1
R: F-actin-binding Coiled-Coil domain of LFAT1
S: F-actin-binding Coiled-Coil domain of LFAT1
T: F-actin-binding Coiled-Coil domain of LFAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,49740
Polymers491,98220
Non-polymers4,51520
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41227.035 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P68138, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
F-actin-binding Coiled-Coil domain of LFAT1


Mass: 7971.139 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg1387 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZVQ3
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
11:1 complex LFAT1's FCC domain with F-actinCOMPLEX#1-#20RECOMBINANT
2Alpha actin from Bovine skeletal muscleCOMPLEX#11NATURAL
3F-actin-binding Coiled-coil domain of the LFAT1 effector from Legionella pneumohilaCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Legionella pneumophila (bacteria)446
32Bos taurus (domestic cattle)9913
43Legionella pneumophila (bacteria)446
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMTris-HCl1
20.2 mMCalcium chlorideCaCl21
30.2 mMATP1
40.5 mMDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal magnification: 100000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3000 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.23 sec. / Electron dose: 40.68 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4548
Image scansWidth: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraX1.25model fitting
11cryoSPARCclassification
12cryoSPARC33D reconstruction
13PHENIX9model refinement
Image processingDetails: movies were motion-corrected and CTF estimation calculations were performed
CTF correctionType: NONE
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
11-16728C1
21-16728C1
31-16728C1
Particle selectionNum. of particles selected: 1733108
Details: particles were automatically picked via the helical tracer tool from CryoSparc
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1220462 / Num. of class averages: 12 / Symmetry type: HELICAL
Atomic model buildingB value: 144 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: cross-correlation coefficient
Details: Initial models were docked using Chimera's rigid-body fitting followed by real-space refinement in PHENIX
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11AF-Q5ZVQ3-F11AlphaFoldin silico model
21AF-P68138-F12AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00335420
ELECTRON MICROSCOPYf_angle_d0.58547990
ELECTRON MICROSCOPYf_dihedral_angle_d5.0514840
ELECTRON MICROSCOPYf_chiral_restr0.045430
ELECTRON MICROSCOPYf_plane_restr0.0056110

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