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- EMDB-42775: Acinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42775
TitleAcinetobacter baumannii Tse15 Rhs effector, toxin cleavage mutant (D1369N, D1391N)
Map data
Sample
  • Organelle or cellular component: Recombinant Tse15(D1369N, D1391N) protein
    • Protein or peptide: Tse15
KeywordsRhs-effector / Rhs cargo effector / Type 6 secretion system effector / Acinetobacter baumannii toxin / YD-repeat protein / T6SS. / TOXIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds / hydrolase activity
Similarity search - Function
RHS protein / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii AB307-0294 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.77 Å
AuthorsHayes BK / Venugopal H / McGowan S
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1165036 Australia
National Health and Medical Research Council (NHMRC, Australia)1128981 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery.
Authors: Brooke K Hayes / Marina Harper / Hariprasad Venugopal / Jessica M Lewis / Amy Wright / Han-Chung Lee / Joel R Steele / David L Steer / Ralf B Schittenhelm / John D Boyce / Sheena McGowan /
Abstract: The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins into adjacent cells. Here we present the structure of Tse15, a T6SS ...The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins into adjacent cells. Here we present the structure of Tse15, a T6SS Rhs effector from the nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered β-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain inside the Rhs cage. Tse15 is cleaved into three domains, through independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for N-terminal clade cleavage. Proteomic analyses identified that significantly more peptides from the N-terminal clade and toxin domains were secreted than from the Rhs cage, suggesting toxin delivery often occurs without the cage. We propose the clade domain acts as an internal chaperone to mediate toxin tethering to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggests this may be a common mechanism for delivery.
History
DepositionNov 10, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42775.png

Downloads & links

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Map

FileDownload / File: emd_42775.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.259
Minimum - Maximum-0.7602507 - 1.9959499
Average (Standard dev.)-0.0022595522 (±0.046868093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42775_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42775_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42775_half_map_2.map
Projections & Slices
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Sample components

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Entire : Recombinant Tse15(D1369N, D1391N) protein

EntireName: Recombinant Tse15(D1369N, D1391N) protein
Components
  • Organelle or cellular component: Recombinant Tse15(D1369N, D1391N) protein
    • Protein or peptide: Tse15

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Supramolecule #1: Recombinant Tse15(D1369N, D1391N) protein

SupramoleculeName: Recombinant Tse15(D1369N, D1391N) protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 183 KDa

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Macromolecule #1: Tse15

MacromoleculeName: Tse15 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 181.545062 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAKENTQQKE IKRQPAVELA VFNLNSVTDV ADLQMIASQV QLYLQVCGNT TLEQIKSKAN ITTVANIFAL TGSVLDLMLY ATDKKTGDA AVQRGALLAA NLIGLFSEPN NEAHARMALR PMFGLMAECL YRENGKIKET DIKRLGLHLN AMIAGDLENF L KETQAKLS ...String:
MAKENTQQKE IKRQPAVELA VFNLNSVTDV ADLQMIASQV QLYLQVCGNT TLEQIKSKAN ITTVANIFAL TGSVLDLMLY ATDKKTGDA AVQRGALLAA NLIGLFSEPN NEAHARMALR PMFGLMAECL YRENGKIKET DIKRLGLHLN AMIAGDLENF L KETQAKLS SLLISATTLG VTILQSMATP ATGINAGITT AAGASAEKRD PKLKFTNWAV PLIDLLGKPS QANLTPKIQP NI TSRLQQE ATQAIAALSQ TLQQQANAGQ KYTLAWLLQE TLKAIQALEN KGNASVPINQ TGEYERHTKG DTLEFVSLQA DAL NAPPCE GADSQSGKSI SYSIGAERVQ HADFYLPKIG FSFIRQYNSQ MDEFDQSMVG ARWMMPFSNM IQQNAQGYLF IDSK GRKHQ LPVSIIFETY EVPYEGWIIK PLKNGELILD FGGEWRSHFQ SFDGGKNYYL VKKMNETSQE EILLEYLLLD HIAYL KVIN FKLKQAEYEL KFAFNEQVKI IAVFLDDKAE PLARYEYDTQ GNLIKAIDQN GHTRTYEYNQ FHQLTRYTDR TGRGQN IRY ESTEAKAKAI EEWADDGSFH TKLKWHPRLR QVAVYDAYDV PTYYYFDLDG FTYRTRLADG RESWYSRDGK KRITRQI DF DGRETQQEYN DQDQLVKIVQ PNGGIIRFAY NKQGNLVEIK DPEGSIWKRE YDENRNVSKE INPLGHITQY KYNNDNQL V EVIDAKGGVK KIQYNELGQM ISYTDCSGKS STWEYDEDGA LTAEQTANNK VVQYFYSTKG RDKGQLQSII YPDGLKEYF EHDEEGRLLK HTDTKGLVTE YKYNQVGLLE QRIDANRHSV AYQWDKQGRI QKLINQNQAE YLFGYNPYGY LIREQAFDGE EKHYSYNEN GRLFQIRRPN ILTQFDYYAD GQIASKSFTH LHTGQKQTEQ FDYNLNSQLS RASNEVSQID LYRNALGQLV R EHQHYKIP ELKPLTAVLH YEYDELGNLI KTIRPDGHTL NHLVYGSGHI YAIGLNNQEV VSFQRDDLHR ETTRLLANGL MQ TKQYNDV GLLSSQFIQP EQETQDYLQY QAHRKYHYDK NYLLSQVEDS RLGKLNYQYD PIGRLIAAQS LHKTESFNFD PAG NLIDSE SVLSPAQIKN NLIKSYKGKH YQYDVQGNVT EIIQAGKNLK LTWDNQNRLI RSDNNGLVTE YGYDVFGRRL YKKT AKELT LFGWDGDLMI WESFKSAQTN YTKHYIYEPD SFVPLLQAGY KDFIQLIETP DYQEYQTKPY SIYKDPVWNR NLGKE RTAL EQFTFYHCDQ VGTPQTMTNI RGECVWEILQ DTWGAVSQIK ALNQDNPFEQ NNLRFQGQYY DRETELHYNR YRYYEP HSA RYVSKNPIGL EGGMNTSSYV SDPNQWINPK GLNSFNYGEM FGIPASAQSG LAYQGQRNYE CYAETGELCK IKVPPLF DY VACSGGGLGI GVGFVKNQWT GEYYISGSKD SLLIPVAKSV AQNKQFSAKD LAGASCVGGN IHNIPSYTKT TMTMGEIT N EFVSGASVTV GGGAYGAVAN VVVPLVSKSS PVKGTWASEL GVGTPGFNVG VSGTVSVDTI LDAVKPSKKH HHHHH

UniProtKB: Tse15

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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 / Details: 50 mM Hepes pH 8.0; 300 mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1163105
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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