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Yorodumi- EMDB-9341: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -
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-Basic information
Entry | Database: EMDB / ID: EMD-9341 | |||||||||
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Title | Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - full map sharpened | |||||||||
Map data | Type VI secretion system TssK-TssF-TssG baseplate subcomplex, sharpened map | |||||||||
Sample |
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Keywords | Type VI secretion system / enteroaggregative E. coli / protein secretion / baseplate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / PROTEIN TRANSPORT | |||||||||
Function / homology | Type VI secretion system TssF / Type VI secretion system, TssF / Type VI secretion, TssG-like / Type VI secretion, TssG / Type VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion protein / Type VI secretion protein / Putative type VI secretion protein Function and homology information | |||||||||
Biological species | Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Park YJ / Lacourse KD / Cambillau C / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / Mougous JD / Veesler D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy. Authors: Young-Jun Park / Kaitlyn D Lacourse / Christian Cambillau / Frank DiMaio / Joseph D Mougous / David Veesler / Abstract: Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although ...Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9341.map.gz | 6.9 MB | EMDB map data format | |
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Header (meta data) | emd-9341-v30.xml emd-9341.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_9341.png | 142.9 KB | ||
Filedesc metadata | emd-9341.cif.gz | 6.5 KB | ||
Others | emd_9341_additional.map.gz | 71.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9341 | HTTPS FTP |
-Related structure data
Related structure data | 6n38MC 9342C 9343C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9341.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Type VI secretion system TssK-TssF-TssG baseplate subcomplex, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Type VI secretion system TssK-TssF-TssG baseplate subcomplex, unsharpened...
File | emd_9341_additional.map | ||||||||||||
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Annotation | Type VI secretion system TssK-TssF-TssG baseplate subcomplex, unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TssK-TssF-TssG T6SS baseplate subcomplex
Entire | Name: TssK-TssF-TssG T6SS baseplate subcomplex |
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Components |
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-Supramolecule #1: TssK-TssF-TssG T6SS baseplate subcomplex
Supramolecule | Name: TssK-TssF-TssG T6SS baseplate subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) |
-Macromolecule #1: Putative type VI secretion protein
Macromolecule | Name: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) Strain: 042 / EAEC |
Molecular weight | Theoretical: 66.557125 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW ...String: MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW SQVDLHRLSL YLAAEAPVSS TLHLMMTKRL AALYLRLPGN DERIRIDGWF SPGGFAEEDR LWPKGDSAFS GY QLLLEYF TFREKFMFVH LNGLENVSLP AGISGFDLEV VLSQPWPADL PVTDDALCLH CVPVINLFTL EADPLIINGL ESE YLLRPK RLQDGYTEIY SVDAVTGSGR TGSAEYVPFT SFRHRGGMLR HDAPERYYHT RVKRGVTGMY DTWLILGGQR WEAD RMPER ETLSLRITGT NGQLPRRALQ STLLDRCEQV LQAPVSVRNL CKPTLPVYPP TEDRFHWRVM SHLGTGFLNM LSSAE VLRG TLALYNWRDD ELNHRRLDAI LAVQHHRIQR FEKGFLLRGL DVEVTLDGNG FAGEGDIHLF GEMLNRFLAL YADMNQ FNQ LTLIVQPEGK CIRWKENHNP RLPG UniProtKB: Type VI secretion protein |
-Macromolecule #2: Putative type VI secretion protein
Macromolecule | Name: Putative type VI secretion protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) Strain: 042 / EAEC |
Molecular weight | Theoretical: 33.787875 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGFPASEIKD AVIPEESHLP PIVHVTFMGL YGVTSPLPAH YISDIAQQRE GHEAAADFLD IFSHRLITQY YRIWRKYSYP ATFEAGGQD KTSQYLLGLA RLGIPGCAQN IATPVSRFLA LLPLMLLPGR TAEGLTSLVT LLAPGTQARV WHHDRRRIPL K TPLTMRVH ...String: MGFPASEIKD AVIPEESHLP PIVHVTFMGL YGVTSPLPAH YISDIAQQRE GHEAAADFLD IFSHRLITQY YRIWRKYSYP ATFEAGGQD KTSQYLLGLA RLGIPGCAQN IATPVSRFLA LLPLMLLPGR TAEGLTSLVT LLAPGTQARV WHHDRRRIPL K TPLTMRVH HPVSLKSRPV MGDHATDVNG QVLLQLSTQT GSEVQGWLPG GHLYSDLLAL LHVYLGSRLD VRLQLCVERS LL PDARLSC RPAAGSPQLG RTAVMRTQAK IATSAARVMT ISLGRYQRVQ EHYQRKETQE NGDYRW UniProtKB: Putative type VI secretion protein |
-Macromolecule #3: Unassigned protein
Macromolecule | Name: Unassigned protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) Strain: strain 042 / EAEC |
Molecular weight | Theoretical: 1.805216 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK) |
-Macromolecule #4: Putative type VI secretion protein
Macromolecule | Name: Putative type VI secretion protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria) Strain: 042 / EAEC |
Molecular weight | Theoretical: 36.57768 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT ...String: MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT RLVRDAQGQW CRDPRFIPPL LTLSASPSLM TELAELLHHL QARRQRLMSM RRENNARLAD FAVADVSLFW LL NALNSAE PVLKELLDMP YRHPELLYRE LARLAGSLLT FSLEHNVDAV PAYHHETPEN VFPPLLSLLN RLLEASLPSH HHH HH UniProtKB: Type VI secretion protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.12 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: An initial model was obtained using cryosparc abinitio. |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36496 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0) |