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- EMDB-36294: Legionella effector protein SidI -

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ID or keywords:

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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
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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: Subramanian A / Wang L / Moss T / Voorhies M / Sangwan S / Stevenson E / Pulido EH / Kwok S / Chalkley RJ / Li KH / Krogan NJ / Swaney DL / Burlingame AL / Floor SN / Sil A / Walter P / Mukherjee S
History
DepositionMay 25, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 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)
Voxel sizeX=Y=Z: 0.844 Å
Density
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
AxesZYX

Projections

Slices (1/2)
Density Histograms

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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 749000

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