+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20695 | |||||||||
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Title | Structure of PdpA-VgrG Complex, Lidless | |||||||||
Map data | PdpA-VgrG Complex, Lidless | |||||||||
Sample |
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Keywords | T6SS Central Spike / Complex / TRANSPORT PROTEIN | |||||||||
Function / homology | Uncharacterized protein / PdpA Function and homology information | |||||||||
Biological species | Francisella novicida (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.21 Å | |||||||||
Authors | Yang X / Clemens DL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2019 Title: Atomic Structure of the Francisella T6SS Central Spike Reveals a Unique α-Helical Lid and a Putative Cargo. Authors: Xue Yang / Daniel L Clemens / Bai-Yu Lee / Yanxiang Cui / Z Hong Zhou / Marcus A Horwitz / Abstract: Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms ...Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms involved are unknown. Here we report the atomic structure of the Francisella T6SS central spike complex, obtained by cryo-electron microscopy. Our structural and functional studies demonstrate that, unlike the single-protein spike composition of other T6SS subtypes, Francisella T6SS's central spike is formed by two proteins, PdpA and VgrG, akin to T4-bacteriophage gp27 and gp5, respectively, and that PdpA has unique characteristics, including a putative cargo within its cavity and an N-terminal helical lid. Structure-guided mutagenesis demonstrates that the PdpA N-terminal lid and C-terminal spike are essential to Francisella T6SS function. PdpA is thus both an adaptor, connecting VgrG to the tube, and a likely carrier of secreted cargo. These findings are important to understanding Francisella pathogenicity and designing therapeutics to combat tularemia. | |||||||||
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_20695.map.gz | 11.3 MB | EMDB map data format | |
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Header (meta data) | emd-20695-v30.xml emd-20695.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_20695.png | 75.1 KB | ||
Filedesc metadata | emd-20695.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20695 | HTTPS FTP |
-Validation report
Summary document | emd_20695_validation.pdf.gz | 354.6 KB | Display | EMDB validaton report |
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Full document | emd_20695_full_validation.pdf.gz | 354.1 KB | Display | |
Data in XML | emd_20695_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_20695_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20695 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20695 | HTTPS FTP |
-Related structure data
Related structure data | 6u9eMC 6u9fC 6u9gC 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_20695.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PdpA-VgrG Complex, Lidless | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PdpA-VgrG complex
Entire | Name: PdpA-VgrG complex |
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Components |
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-Supramolecule #1: PdpA-VgrG complex
Supramolecule | Name: PdpA-VgrG complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Francisella novicida (bacteria) |
-Macromolecule #1: PdpA
Macromolecule | Name: PdpA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Francisella novicida (bacteria) |
Molecular weight | Theoretical: 95.469961 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIAVKDITDL NIQDIISQLT SEVINGDTTP SSAKFACEIN SYIINYNLSN INLINTQLKN TKILYRKGLI SKLDYEKYKR YCIISRFKN NIDEFILYFS TNYKDSQSLK IAIKELQNSC SSSLILELPH DYIRKIDVLL TSIDSAIQRS SDLNKTIIKQ L NKLRSSLS ...String: MIAVKDITDL NIQDIISQLT SEVINGDTTP SSAKFACEIN SYIINYNLSN INLINTQLKN TKILYRKGLI SKLDYEKYKR YCIISRFKN NIDEFILYFS TNYKDSQSLK IAIKELQNSC SSSLILELPH DYIRKIDVLL TSIDSAIQRS SDLNKTIIKQ L NKLRSSLS RYIGYNNVLQ KQEITINIKP INKNFELEDI SFVSTRNKQY FKHNSLTLKN PHIEKLEVCE NIYGINGWLT FD LAYINNH KDFNFLLSPN QPILLDIQIN DSFNFYKKES KKDHHKRTTR FIAIGFNSNS IDIHENFEYS IYSYTKNVSS GVK KFKIQF HDPLKALWTK HKPSYIALNK SLDDIFKDNF FFDSLFSLDT NKSNNLKIRI PQAFISTVNR NFYDFFIQQL EQNK CYLKY FCDKKSGKVS YHVVDQVDND LQRNIVNSDE DLKDKLSPYD ISCFKKQILI SNKSNFYVKE KNICPDVTLN TQRKE DRKI SDTLVKPFSS ILKDNLQSVE YIQSNNDDKQ EIITTGFEIL LTSRNTLPFL DTEITLSKLD NDQNYLLGAT DIKSLY ISQ RKLLFKRSKY CSKQLYENLH NFHYKSDSES DVYEKIAFTK YPSLTHDNSI TYKIKDYSNL TPEYPKYKSF SNFYING RI TIGENVNNDS KKAYKFFKNH KPEESSIAEF QENGEKGTSA ILNSKADILY AIEIAKEMLS DKSSDKPIIY LPLKVNIN S ANNQFIPLRN DDIILIEIQS FTKGEIIELI SNSAISTKKA QQQLLQRQLL GSKENCEMAY TQTSDSETFS LTQVNEDCE NSFLINDKKG IFLRYKSKGN UniProtKB: PdpA |
-Macromolecule #2: VgrG
Macromolecule | Name: VgrG / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Francisella novicida (bacteria) |
Molecular weight | Theoretical: 20.539779 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDYKDDDDKD YKDDDDKDYK DDDDKGSKAD HIFNLEEQGL LIDIKDDSKG CTTKLESSGK ITHNATESIE SSADKQIIEN VKDSKISIT EKEILLATKK SSIMLSEDKI VIKIGNSLII LDDSNISLES ATINIKSSAN INIQASQNID IKSLNNSIKA D VNLNAEGL DVNIKGSVTA SIKGSAATMV G UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Details: unspecified |
Vitrification | Cryogen name: ETHANE / 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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16889 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6u9e: |