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- EMDB-36454: Cryo-EM structure of a Legionella effector complexed with actin a... -

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Basic information

Entry
Database: EMDB / ID: EMD-36454
TitleCryo-EM structure of a Legionella effector complexed with actin and AMP
Map data
Sample
  • Complex: Cryo-EM structure of a Legionella effector complexed with actin and AMP
    • Protein or peptide: Substrate of the Dot/Icm secretion system
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAMPylation / TOXIN
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein 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
Substrate of the Dot/Icm secretion system / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesLegionella sainthelensi (bacteria) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsZhou XT / Wang XF / Tan JX / Zhu YQ
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)21974002 China
National Natural Science Foundation of China (NSFC)22174003 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: To Be Published
Title: Cryo-EM structure of a Legionella effector complexed with actin and AMP
Authors: Zhou XT / Wang XF / Tan JX / Zhu YQ
History
DepositionJun 7, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36454.png

Downloads & links

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Map

FileDownload / File: emd_36454.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.648
Minimum - Maximum-6.039572 - 9.584440000000001
Average (Standard dev.)-0.00176584 (±0.15112671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36454_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_36454_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 : Cryo-EM structure of a Legionella effector complexed with actin a...

EntireName: Cryo-EM structure of a Legionella effector complexed with actin and AMP
Components
  • Complex: Cryo-EM structure of a Legionella effector complexed with actin and AMP
    • Protein or peptide: Substrate of the Dot/Icm secretion system
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of a Legionella effector complexed with actin a...

SupramoleculeName: Cryo-EM structure of a Legionella effector complexed with actin and AMP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Legionella sainthelensi (bacteria)

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Macromolecule #1: Substrate of the Dot/Icm secretion system

MacromoleculeName: Substrate of the Dot/Icm secretion system / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella sainthelensi (bacteria)
Molecular weightTheoretical: 50.62148 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSYTKIESSL LLALDYPKLD ESDFILLLTK FLEKKLGNND NYPTFSKQIQ KYYLEQEYKK AIENILRLCQ ENETLLGTNL VQRLITKSS QVTSNPKDNE SRRFYEVLYA EHLESILRKD FDCSIFDELN EAYNEVRPEY TVNDLTKINT FEEARKLILA F VMLNDNVE ...String:
MSYTKIESSL LLALDYPKLD ESDFILLLTK FLEKKLGNND NYPTFSKQIQ KYYLEQEYKK AIENILRLCQ ENETLLGTNL VQRLITKSS QVTSNPKDNE SRRFYEVLYA EHLESILRKD FDCSIFDELN EAYNEVRPEY TVNDLTKINT FEEARKLILA F VMLNDNVE LGLKAQSAIY QKKDRSREEL GQVLTANPGI MKPNSPNFAD NTVPIKKIDK IAIDEKKAGG YSKTNPQVPF VA SLSGTTY SLVVVLQKYM DKHKTDPNLE KKINNIVMLW TSAYIKDGYH SYKEVIDIFK DAHIQSIFAR ANIKLDYAII DDT DHEFHR AQEYTQGIAT KAMMHQELVQ KVQEKSMREE KQKQMLLFCG VLVNQLNQDP KSKEKYPEQL ESLNALYKNW NAGT IKNQE FKKECTQVCT EIQIKEQNTP SSGWSHPQFE K

UniProtKB: Substrate of the Dot/Icm secretion system

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #3: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 868128

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo built model
Output model

PDB-8jo3:
Cryo-EM structure of a Legionella effector complexed with actin and AMP

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