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Yorodumi- EMDB-11827: Nonameric cytoplasmic domain of FlhA from Vibrio parahaemolyticus -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11827 | ||||||||||||||||||
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Title | Nonameric cytoplasmic domain of FlhA from Vibrio parahaemolyticus | ||||||||||||||||||
Map data | postprocessed map | ||||||||||||||||||
Sample |
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Keywords | T3SS / export apparatus / secretion / protein export / motility / PROTEIN TRANSPORT | ||||||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | ||||||||||||||||||
Authors | Kuhlen L / Johnson S | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: PLoS One / Year: 2021 Title: Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein. Authors: Lucas Kuhlen / Steven Johnson / Jerry Cao / Justin C Deme / Susan M Lea / Abstract: Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which ...Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomer's cytoplasmic domain, which stabilises the nonameric ring assembly. | ||||||||||||||||||
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_11827.map.gz | 265.8 MB | EMDB map data format | |
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Header (meta data) | emd-11827-v30.xml emd-11827.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11827_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_11827.png | 191.2 KB | ||
Masks | emd_11827_msk_1.map | 290.8 MB | Mask map | |
Filedesc metadata | emd-11827.cif.gz | 5.7 KB | ||
Others | emd_11827_half_map_1.map.gz emd_11827_half_map_2.map.gz | 231.8 MB 231.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11827 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11827 | HTTPS FTP |
-Validation report
Summary document | emd_11827_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_11827_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_11827_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_11827_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11827 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11827 | HTTPS FTP |
-Related structure data
Related structure data | 7amyMC 7alwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11827.map.gz / Format: CCP4 / Size: 290.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11827_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_11827_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_11827_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nonamer of the FlhA cytoplasmic domain from Vibrio parahaemolyticus
Entire | Name: Nonamer of the FlhA cytoplasmic domain from Vibrio parahaemolyticus |
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Components |
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-Supramolecule #1: Nonamer of the FlhA cytoplasmic domain from Vibrio parahaemolyticus
Supramolecule | Name: Nonamer of the FlhA cytoplasmic domain from Vibrio parahaemolyticus type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio parahaemolyticus (bacteria) |
Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: Flagellar biosynthesis protein FlhA
Macromolecule | Name: Flagellar biosynthesis protein FlhA / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio parahaemolyticus (bacteria) |
Molecular weight | Theoretical: 76.55582 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MLTRLKQLQT STKGYIGIPI VLLMILAMVI LPLPPLLLDA LFTFNIVLAI LVLLVSTTAK RPLDFSVFPT ILLVATLLRL TLNVASTRI VLLEGHNGGD AAGKVIQAFG EVVIGGNYVV GMVVFIILMI INFVVITKGG ERISEVSARF TLDALPGKQM A IDADLNAG ...String: MLTRLKQLQT STKGYIGIPI VLLMILAMVI LPLPPLLLDA LFTFNIVLAI LVLLVSTTAK RPLDFSVFPT ILLVATLLRL TLNVASTRI VLLEGHNGGD AAGKVIQAFG EVVIGGNYVV GMVVFIILMI INFVVITKGG ERISEVSARF TLDALPGKQM A IDADLNAG LIDQETARLR RKEVANEADF HGSMDGASKF VRGDAVAGLL ILFINIIGGI SIGVFEHGLP ASEAFKTYAL LT IGDGLVA QIPSLLLATA AAIIVTRIND SDNGMSETMQ KQLLATPATL FTVAGIMAVI GMVPGMPHLA FFAFAGALGF AGW RQSKKP VQDTQIEQVE ALSQAMQEED TPLTWDDIPH VHTLSLALGY RLVHLVNKDQ GAPLSQRIRG VRRNLSEQVG FLLP EVRIR DNLSLKPNQY TISLNGEVIE QGFIEPERLM AIAVGDTYGE IDGILGSDPA YQLPAVWIEH QDKAKALNMG YQVVD DGTV IATHISKIMK TNLAELFTHD DVEAMTQRLT QQAPKLAEAL AAALNPAQQL KVYRQLLLDQ VPLKDIRTIA NTMLES SEN TKDPILLAAD VRCALKRTLV NLIAGQKPEL NVYALSDELE QMLLTSLQQA QASGTVVLDS FPIEPNILGQ FQQNLPL IR QQLKQQGLPP ILLVMPQLRP LLARYARTFT QGLAVLSYNE IPENKQINVV GNLGENLYFQ UniProtKB: Flagellar biosynthesis protein FlhA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-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: 48.0 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 |