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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0264 | |||||||||
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Title | Type VI membrane complex | |||||||||
![]() | MolRes Sharpened map | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rapisarda C / Fronzes R | |||||||||
![]() | ![]() Title: and high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex. Authors: Chiara Rapisarda / Yassine Cherrak / Romain Kooger / Victoria Schmidt / Riccardo Pellarin / Laureen Logger / Eric Cascales / Martin Pilhofer / Eric Durand / Rémi Fronzes / ![]() ![]() Abstract: Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is ...Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to phages. It is composed of a phage tail-like structure inserted in the bacterial cell envelope by a membrane complex (MC) comprising the TssJ, TssL and TssM proteins. We previously reported the low-resolution negative-stain electron microscopy structure of the enteroaggregative MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analyses of the T6SS MC confirm the 5-fold symmetry and identify the regions of the structure that insert into the bacterial membranes. A high-resolution model obtained by single-particle cryo-electron microscopy highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, an 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we propose an updated model on MC structure and dynamics during T6SS assembly and function. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 372.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
Images | ![]() | 164.1 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() ![]() | 377.2 MB 380.6 MB 381.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hs7MC ![]() 0265C ![]() 0266C ![]() 0267C ![]() 4561C ![]() 4562C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | MolRes Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Refinement map
File | emd_0264_additional.map | ||||||||||||
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Annotation | Refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_0264_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_0264_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Membrane complex of the type VI secretion system (TssM and TssJ)
Entire | Name: Membrane complex of the type VI secretion system (TssM and TssJ)![]() |
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Components |
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-Supramolecule #1: Membrane complex of the type VI secretion system (TssM and TssJ)
Supramolecule | Name: Membrane complex of the type VI secretion system (TssM and TssJ) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: ImcF-like family protein
Macromolecule | Name: ImcF-like family protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 127.255367 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAFLGAETR RDQILLLILL SLGLLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGEPSQP E NADWLAAL ...String: MNKLACLSGR FGRPGIVFIG VAALWWLITR YGAFLGAETR RDQILLLILL SLGLLFVCYL PVMKKYVQEL TYRRRARKEQ RLPDDEERL AQTPPRYVTV QDIRHTLRRQ YGRFWGRKIR ILLITGTASE VELLTPGLTE QFWQEEQGTL LLWGGEPSQP E NADWLAAL RRLRYRPADG IVWVTSGLSE TLSAPLTEDA LDRVSRAVSS CCERLGWRLP LYVWSLQESP DERGRITQPV GC LLPAECS SDKLKAQLQA MLPGLVAQGI QQICCAPRYY FLLSLAERFR RNIDAVVEPL SVLLRPYRQL LLAGIVFSPA TVG GERSVR HRWRMDNRWE ALPETVQQLP VRLQPSRTGH NWRRSLAVMA AILMMAQGTG MVVSFLANRS LVAEVQEQIR PAQN QQLSP AERLQALLNL QKSLARLQYR EEHGAPWYLR AGMNQNADLL VVVMPLYAQN AHLLLRDAAA AHLEQQLRTF IRLPP DSPQ RGKMAKAAYD QLRLYLMLAQ PQHMEPAWFS RTLMREWPQR DGVSAVFWQA NGPTLLAYYA SGIITHPQWK LTADEE LVS QSRTLLLRHL GTQNSDAMLY QKMLARVAHQ FADMRLTDMT GDTDVSRLFF TDEVVPGMFT RQAWEEAVLP SIDTVIN ER REEMDWVLTD GRQKAPSPVS PEALRQRLTT RYFADFGNAW LNFLNSLHLR KAQMLSDVTE QLTLMADVRQ SPLVALMN T LAVQGRTGQP REAVTDSLVK SARNLLSQEK QPVAVPESRL HGPLATTFGP VLALMDNQNN SADMLNLQTY LTRVTQVRL RLQQIAGSSD PQAMMQMLAQ TVLQGKSVDL TDTRDYGSLT AAGLGQEWYG FGQTVFVRPM EQAWQQVLTP AAESLNARWR TAVVDGWNN AFSGRYPFKN VSSDASLPLL AKYLNTDTGR IARFLQNNLS GVLHREGSRW VPDTINTRGL TFNPAFLKAI N TLSEIADV AFTTGNAGLH FELRPGTAAG VMQTTLITDN QKLIYVNQMP VWKRFTWPAD TEAPGASLSW VSTQAGTRQY AD LPGSWGL IRLLEMARRK AAPGVASGWS LSWQAQDGRM LNYTLRTEAG EGPLVLLKLR NFVLPETVFE LSGTSAFTGN DED AGDTVE ETD UniProtKB: ImcF-like family protein |
-Macromolecule #2: Type VI secretion system protein VasD
Macromolecule | Name: Type VI secretion system protein VasD / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 20.313236 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MAIIAGKAGY GLIIALFSLS LSGCGLTQRV ADGTVSATKS LFYRQIKTLH LDIRAREAIN TSAAGIPLSV VVRIYQLKDN RSFDSADYQ ALFTGDNEIL AGDIIAQKDV WLQPGGSVAV DMPLDDAAKF TGVAAMFLEP DQKKNTWRVV LGRDELEPDT P RLIEVSGN TLTLLPVKDK WSHPQFEK UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 0.003 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 120.0 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic![]() |