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- EMDB-43087: Actin-binding domain of Legionella pneumophila effector LFAT1 (lp... -

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Basic information

Entry
Database: EMDB / ID: EMD-43087
TitleActin-binding domain of Legionella pneumophila effector LFAT1 (lpg1387) bound to F-actin
Map data
Sample
  • Complex: 1:1 complex LFAT1's FCC domain with F-actin
    • Complex: Alpha actin from Bovine skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: F-actin-binding Coiled-coil domain of the LFAT1 effector from Legionella pneumohila
      • Protein or peptide: F-actin-binding Coiled-Coil domain of LFAT1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsComplex / F-actin binding domain / lysine fatty-acyltransferase / coiled-coil / TOXIN
Function / homology
Function and homology information


Striated Muscle Contraction / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium ...Striated Muscle Contraction / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / hydrolase activity / positive regulation of gene expression / ATP 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
Actin, alpha skeletal muscle / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria) / Bos taurus (domestic cattle)
Methodhelical reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsZeng W / Mao Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM135379-01 United States
CitationJournal: To Be Published
Title: Structural basis for a novel F-actin binding domain from the Legionella pneumophila lysine fatty-acyltransferase LFAT1
Authors: Zeng W / Komaniecki G / Lin H / Mao Y
History
DepositionDec 11, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43087.png

Downloads & links

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Map

FileDownload / File: emd_43087.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 416.5 Å		0.83 Å/pix.
x 500 pix.
= 416.5 Å		0.83 Å/pix.
x 500 pix.
= 416.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.04478782 - 0.33203378
Average (Standard dev.)0.00025453788 (±0.011577759)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 416.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43087_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_43087_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 : 1:1 complex LFAT1's FCC domain with F-actin

EntireName: 1:1 complex LFAT1's FCC domain with F-actin
Components
  • Complex: 1:1 complex LFAT1's FCC domain with F-actin
    • Complex: Alpha actin from Bovine skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: F-actin-binding Coiled-coil domain of the LFAT1 effector from Legionella pneumohila
      • Protein or peptide: F-actin-binding Coiled-Coil domain of LFAT1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: 1:1 complex LFAT1's FCC domain with F-actin

SupramoleculeName: 1:1 complex LFAT1's FCC domain with F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Legionella pneumophila (bacteria)

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Supramolecule #2: Alpha actin from Bovine skeletal muscle

SupramoleculeName: Alpha actin from Bovine skeletal muscle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: F-actin-binding Coiled-coil domain of the LFAT1 effector from Leg...

SupramoleculeName: F-actin-binding Coiled-coil domain of the LFAT1 effector from Legionella pneumohila
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Legionella pneumophila (bacteria)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 41.227035 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSYEL PD GQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITALA PST MKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKC

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: F-actin-binding Coiled-Coil domain of LFAT1

MacromoleculeName: F-actin-binding Coiled-Coil domain of LFAT1 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 7.971139 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DLKGQLAKLE LHLNKTNGQI TATERTINYL NKLKNPDPKT KTQLIELTEK LIKLKQEFET TINSQHEIS

UniProtKB: Uncharacterized protein

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
5.0 mMTris-HCl
0.2 mMCalcium chlorideCaCl2
0.2 mMATP
0.5 mMDTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 4548 / Average exposure time: 1.23 sec. / Average electron dose: 40.68 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Detailsmovies were motion-corrected and CTF estimation calculations were performed
Final reconstructionNumber classes used: 12
Applied symmetry - Helical parameters - Δz: 28.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -167 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 1220462
Segment selectionNumber selected: 1733108 / Software - Name: cryoSPARC
Details: particles were automatically picked via the helical tracer tool from CryoSparc
Startup modelType of model: INSILICO MODEL
In silico model: Low-resolution in-silico model was generated using CryoSparc's Ab-Initio function
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3-f1

source_name: AlphaFold, initial_model_type: in silico model

8-f1

source_name: AlphaFold, initial_model_type: in silico model
DetailsInitial models were docked using Chimera's rigid-body fitting followed by real-space refinement in PHENIX
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 144 / Target criteria: cross-correlation coefficient
Output model

PDB-8vaa:
Actin-binding domain of Legionella pneumophila effector LFAT1 (lpg1387) bound to F-actin

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