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- EMDB-36294: Legionella effector protein SidI -

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Basic information

Entry
Database: EMDB / ID: EMD-36294
TitleLegionella effector protein SidI
Map data
Sample
  • Complex: Legionella pneumophila effector proein SidI
    • Complex: Legionella pneumophila effector protein SidI
    • Protein or peptide: Legionella pneumophila effector protein SidI
Keywordsmannosyltransferase / TOXIN
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
: / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...: / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria) / Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang L / Subramanian A / Mukherjee S / Walter P
Funding support United States, 6 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-2312-17 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032384 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99GM143527-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI135990 United States
The Pew Charitable TrustsA129837 United States
CitationJournal: Nat Cell Biol / Year: 2023
Title: A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response.
Authors: Advait Subramanian / Lan Wang / Tom Moss / Mark Voorhies / Smriti Sangwan / Erica Stevenson / Ernst H Pulido / Samentha Kwok / Robert J Chalkley / Kathy H Li / Nevan J Krogan / Danielle L ...Authors: Advait Subramanian / Lan Wang / Tom Moss / Mark Voorhies / Smriti Sangwan / Erica Stevenson / Ernst H Pulido / Samentha Kwok / Robert J Chalkley / Kathy H Li / Nevan J Krogan / Danielle L Swaney / Alma L Burlingame / Stephen N Floor / Anita Sil / Peter Walter / Shaeri Mukherjee /
Abstract: A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of ...A widespread strategy employed by pathogens to establish infection is to inhibit host-cell protein synthesis. Legionella pneumophila, an intracellular bacterial pathogen and the causative organism of Legionnaires' disease, secretes a subset of protein effectors into host cells that inhibit translation elongation. Mechanistic insights into how the bacterium targets translation elongation remain poorly defined. We report here that the Legionella effector SidI functions in an unprecedented way as a transfer-RNA mimic that directly binds to and glycosylates the ribosome. The 3.1 Å cryo-electron microscopy structure of SidI reveals an N-terminal domain with an 'inverted L' shape and surface-charge distribution characteristic of tRNA mimicry, and a C-terminal domain that adopts a glycosyl transferase fold that licenses SidI to utilize GDP-mannose as a sugar precursor. This coupling of tRNA mimicry and enzymatic action endows SidI with the ability to block protein synthesis with a potency comparable to ricin, one of the most powerful toxins known. In Legionella-infected cells, the translational pausing activated by SidI elicits a stress response signature mimicking the ribotoxic stress response, which is activated by elongation inhibitors that induce ribosome collisions. SidI-mediated effects on the ribosome activate the stress kinases ZAKα and p38, which in turn drive an accumulation of the protein activating transcription factor 3 (ATF3). Intriguingly, ATF3 escapes the translation block imposed by SidI, translocates to the nucleus and orchestrates the transcription of stress-inducible genes that promote cell death, revealing a major role for ATF3 in the response to collided ribosome stress. Together, our findings elucidate a novel mechanism by which a pathogenic bacterium employs tRNA mimicry to hijack a ribosome-to-nuclear signalling pathway that regulates cell fate.
History
DepositionMay 25, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36294.png

Downloads & links

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Map

FileDownload / File: emd_36294.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å		0.84 Å/pix.
x 256 pix.
= 216.064 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.3871741 - 5.1501393
Average (Standard dev.)0.005233813 (±0.1182408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.064 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36294_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_36294_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Legionella pneumophila effector proein SidI

EntireName: Legionella pneumophila effector proein SidI
Components
  • Complex: Legionella pneumophila effector proein SidI
    • Complex: Legionella pneumophila effector protein SidI
    • Protein or peptide: Legionella pneumophila effector protein SidI

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Supramolecule #1: Legionella pneumophila effector proein SidI

SupramoleculeName: Legionella pneumophila effector proein SidI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: Legionella pneumophila effector protein SidI

SupramoleculeName: Legionella pneumophila effector protein SidI / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Legionella pneumophila (bacteria)

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Macromolecule #1: Legionella pneumophila effector protein SidI

MacromoleculeName: Legionella pneumophila effector protein SidI / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: glutathione transferase
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1
Molecular weightTheoretical: 134.883031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP GSMTKIYLLT AP FDEEAKT GDGQYAASLE LGFAENYEHI PCKWLKKDKG DYSIPFPTGT TSIPEETIPS AIVLQPVANE NTVISGYKLK DTV SSPEKA QEVNNKTVSP RTPKIIVKHD NSLQSLTIMD IYSQKPIQFD ESKVDEIIHS LETKKVNLEK AIEDNNAELS KIKK QKSKL AYLTRLYKEN KENIQDYCTL NEYIEAHLFN PKFLSRHEKA LNNFKALKSQ FTGPVNLKEL EKLTDKLTGI KEYSY DFHS NSLPYDLEHD KSFRNFYDFD GLKESIESII KELEVLNSIR QAVSDKYPNS FKALNETEEH DDKLKFINII FNDGFS TTY DQQTFIKALS ALDIEKAIDA YTNVKNKLEN TQDIIANKEG CRNKLISELQ TLIANKQEPY LSANEKLGGF YSKRKLS AS EGFHLAYQAN RRDPIKPEVI ENIITKMKPI DEDTHLDIHI RPPDCGVFIT PEDIKKFQEA GIKVNITIHE YKQNYTRR Y LQQYTHDLMR QANSVQFFNA EDRENAIIAA TYGDCDKRNT TEPTGVAKKI REVGEDFDLD KYPVQKYDLK GKSGLTVAS QKLSTEPDHP LDVVAKAPNI LSFGTIRPGK GFEEALKLAQ LIKDNSLSIH EKIKRVPIVK LAGDPQDKAL MKQIVVERFG KTAVKTYQK THPYDNRFNN SQRRDYWKNL VRELNAKVKE EVAVLNNPYI EIYPWCEPHE LLDLKQNCKY VCRMDDMGMR N NGSAIISV LDVGVVYTKF GSVTDDIFIK GGKYGNAVDI GEYRYGKYSL LKKEKEFKEQ HEEEPLPKWL IKNPDSAYKR QS ESRDPKD ILDSIVAREE NQLICDNIED SDNYRTVVEA QKLLKERFTL KNAVDHLLEN IGLGHLIAQE EVDELFETVD PVQ AQIDNL DILSDIKTPR LCLSRSCPEL GFFGSRRGDL EAKQENNKLK ESILVF

UniProtKB: Glutathione S-transferase class-mu 26 kDa isozyme, Uncharacterized protein

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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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 749000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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