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- EMDB-42792: Acinetobacter baumannii Tse15 Rhs effector -

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Basic information

Entry
Database: EMDB / ID: EMD-42792
TitleAcinetobacter baumannii Tse15 Rhs effector
Map data
Sample
  • Organelle or cellular component: Recombinant Tse15
    • Protein or peptide: Tse15
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
KeywordsRhs-effector / Rhs cargo effector / Type 6 secretion system effector / Acinetobacter baumannii toxin / Type VI secretion system / 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: 3.08 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 13, 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_42792.png

Downloads & links

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Map

FileDownload / File: emd_42792.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 224 pix.
= 210.56 Å		0.94 Å/pix.
x 224 pix.
= 210.56 Å		0.94 Å/pix.
x 224 pix.
= 210.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.671
Minimum - Maximum-0.9228442 - 2.6014717
Average (Standard dev.)0.016211482 (±0.10336461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 210.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42792_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Difference map generated in Chimera after refinement of...

Fileemd_42792_additional_1.map
AnnotationDifference map generated in Chimera after refinement of A-chain. Used to guide modelling of unsequenced toxin in chains B, C, D, E.
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_42792_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_42792_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Recombinant Tse15

EntireName: Recombinant Tse15
Components
  • Organelle or cellular component: Recombinant Tse15
    • Protein or peptide: Tse15
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)
    • Protein or peptide: Tse15 toxin peptide (polyUNK)

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Supramolecule #1: Recombinant Tse15

SupramoleculeName: Recombinant Tse15 / 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: 182.818422 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAWSHPQFEK SAAKENTQQK EIKRQPAVEL AVFNLNSVTD VADLQMIASQ VQLYLQVCGN TTLEQIKSKA NITTVANIFA LTGSVLDLM LYATDKKTGD AAVQRGALLA ANLIGLFSEP NNEAHARMAL RPMFGLMAEC LYRENGKIKE TDIKRLGLHL N AMIAGDLE ...String:
MAWSHPQFEK SAAKENTQQK EIKRQPAVEL AVFNLNSVTD VADLQMIASQ VQLYLQVCGN TTLEQIKSKA NITTVANIFA LTGSVLDLM LYATDKKTGD AAVQRGALLA ANLIGLFSEP NNEAHARMAL RPMFGLMAEC LYRENGKIKE TDIKRLGLHL N AMIAGDLE NFLKETQAKL SSLLISATTL GVTILQSMAT PATGINAGIT TAAGASAEKR DPKLKFTNWA VPLIDLLGKP SQ ANLTPKI QPNITSRLQQ EATQAIAALS QTLQQQANAG QKYTLAWLLQ ETLKAIQALE NKGNASVPIN QTGEYERHTK GDT LEFVSL QADALNAPPC EGADSQSGKS ISYSIGAERV QHADFYLPKI GFSFIRQYNS QMDEFDQSMV GARWMMPFSN MIQQ NAQGY LFIDSKGRKH QLPVSIIFET YEVPYEGWII KPLKNGELIL DFGGEWRSHF QSFDGGKNYY LVKKMNETSQ EEILL EYLL LDHIAYLKVI NFKLKQAEYE LKFAFNEQVK IIAVFLDDKA EPLARYEYDT QGNLIKAIDQ NGHTRTYEYN QFHQLT RYT DRTGRGQNIR YESTEAKAKA IEEWADDGSF HTKLKWHPRL RQVAVYDAYD VPTYYYFDLD GFTYRTRLAD GRESWYS RD GKKRITRQID FDGRETQQEY NDQDQLVKIV QPNGGIIRFA YNKQGNLVEI KDPEGSIWKR EYDENRNVSK EINPLGHI T QYKYNNDNQL VEVIDAKGGV KKIQYNELGQ MISYTDCSGK SSTWEYDEDG ALTAEQTANN KVVQYFYSTK GRDKGQLQS IIYPDGLKEY FEHDEEGRLL KHTDTKGLVT EYKYNQVGLL EQRIDANRHS VAYQWDKQGR IQKLINQNQA EYLFGYNPYG YLIREQAFD GEEKHYSYNE NGRLFQIRRP NILTQFDYYA DGQIASKSFT HLHTGQKQTE QFDYNLNSQL SRASNEVSQI D LYRNALGQ LVREHQHYKI PELKPLTAVL HYEYDELGNL IKTIRPDGHT LNHLVYGSGH IYAIGLNNQE VVSFQRDDLH RE TTRLLAN GLMQTKQYND VGLLSSQFIQ PEQETQDYLQ YQAHRKYHYD KNYLLSQVED SRLGKLNYQY DPIGRLIAAQ SLH KTESFN FDPAGNLIDS ESVLSPAQIK NNLIKSYKGK HYQYDVQGNV TEIIQAGKNL KLTWDNQNRL IRSDNNGLVT EYGY DVFGR RLYKKTAKEL TLFGWDGDLM IWESFKSAQT NYTKHYIYEP DSFVPLLQAG YKDFIQLIET PDYQEYQTKP YSIYK DPVW NRNLGKERTA LEQFTFYHCD QVGTPQTMTN IRGECVWEIL QDTWGAVSQI KALNQDNPFE QNNLRFQGQY YDRETE LHY NRYRYYEPHS ARYVSKDPIG LEGGMNTSSY VSDPNQWIDP KGLNSFNYGE MFGIPASAQS GLAYQGQRNY ECYAETG EL CKIKVPPLFD YVACSGGGLG IGVGFVKNQW TGEYYISGSK DSLLIPVAKS VAQNKQFSAK DLAGASCVGG NIHNIPSY T KTTMTMGEIT NEFVSGASVT VGGGAYGAVA NVVVPLVSKS SPVKGTWASE LGVGTPGFNV GVSGTVSVDT ILDAVKPSK KHHHHHH

UniProtKB: Tse15

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Macromolecule #2: Tse15 toxin peptide (polyUNK)

MacromoleculeName: Tse15 toxin peptide (polyUNK) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 2.486056 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Tse15 toxin peptide (polyUNK)

MacromoleculeName: Tse15 toxin peptide (polyUNK) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 954.168 Da
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #4: Tse15 toxin peptide (polyUNK)

MacromoleculeName: Tse15 toxin peptide (polyUNK) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 3.762629 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: Tse15 toxin peptide (polyUNK)

MacromoleculeName: Tse15 toxin peptide (polyUNK) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii AB307-0294 (bacteria)
Molecular weightTheoretical: 2.060531 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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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

Concentration3 mg/mL
BufferpH: 8 / Details: 50 mM Hepes pH 8.0; 300 mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / 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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: 0.5 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 455508
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8xut

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132696
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial fitting with done using UCSF Chimera using fit map.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8uy4:
Acinetobacter baumannii Tse15 Rhs effector

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