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Yorodumi- EMDB-8400: 6.3 Angstrom structure of the Salmonella SPI-1 type III secretion... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8400 | |||||||||
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Title | 6.3 Angstrom structure of the Salmonella SPI-1 type III secretion injectisome basal body | |||||||||
Map data | Single particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion system basal body at 6.3 Angstrom | |||||||||
Sample |
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Keywords | Bacterial / secretion / injectisome / membrane protein | |||||||||
Function / homology | Function and homology information type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Worrall LJ / Hong C | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nature / Year: 2016 Title: Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Authors: L J Worrall / C Hong / M Vuckovic / W Deng / J R C Bergeron / D D Majewski / R K Huang / T Spreter / B B Finlay / Z Yu / N C J Strynadka / Abstract: The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, ...The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 Å and 3.6 Å resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins. | |||||||||
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_8400.map.gz | 85 MB | EMDB map data format | |
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Header (meta data) | emd-8400-v30.xml emd-8400.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
Images | emd_8400.png | 122.8 KB | ||
Filedesc metadata | emd-8400.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8400 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8400 | HTTPS FTP |
-Validation report
Summary document | emd_8400_validation.pdf.gz | 561.9 KB | Display | EMDB validaton report |
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Full document | emd_8400_full_validation.pdf.gz | 561.4 KB | Display | |
Data in XML | emd_8400_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_8400_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8400 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8400 | HTTPS FTP |
-Related structure data
Related structure data | 5tcrMC 8398C 8399C 8401C 5tcpC 5tcqC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8400.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion system basal body at 6.3 Angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.71 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 : Type III injectisome basal body
Entire | Name: Type III injectisome basal body |
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Components |
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-Supramolecule #1: Type III injectisome basal body
Supramolecule | Name: Type III injectisome basal body / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: PrgH130-392 mutant |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 2 MDa |
-Macromolecule #1: Protein InvG
Macromolecule | Name: Protein InvG / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 61.835559 KDa |
Sequence | String: MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKITG NFEFHDPNAL LEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL NEFNNFLKRS GLYNKNYPLR GDNRKGTFYV SGPPVYVDMV V NAATMMDK ...String: MKTHILLARV LACAALVLVT PGYSSEKIPV TGSGFVAKDD SLRTFFDAMA LQLKEPVIVS KMAARKKITG NFEFHDPNAL LEKLSLQLG LIWYFDGQAI YIYDASEMRN AVVSLRNVSL NEFNNFLKRS GLYNKNYPLR GDNRKGTFYV SGPPVYVDMV V NAATMMDK QNDGIELGRQ KIGVMRLNNT FVGDRTYNLR DQKMVIPGIA TAIERLLQGE EQPLGNIVSS EPPAMPAFSA NG EKGKAAN YAGGMSLQEA LKQNAAAGNI KIVAYPDTNS LLVKGTAEQV HFIEMLVKAL DVAKRHVELS LWIVDLNKSD LER LGTSWS GSITIGDKLG VSLNQSSIST LDGSRFIAAV NALEEKKQAT VVSRPVLLTQ ENVPAIFDNN RTFYTKLIGE RNVA LEHVT YGTMIRVLPR FSADGQIEMS LDIEDGNDKT PQSDTTTSVD ALPEVGRTLI STIARVPHGK SLLVGGYTRD ANTDT VQSI PFLGKLPLIG SLFRYSSKNK SNVVRVFMIE PKEIVDPLTP DASESVNNIL KQSGAWSGDD KLQKWVRVYL DRGQEA IK UniProtKB: SPI-1 type 3 secretion system secretin |
-Macromolecule #2: Lipoprotein PrgK
Macromolecule | Name: Lipoprotein PrgK / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 26.199723 KDa |
Sequence | String: CKDKDLLKGL DQEQANEVIA VLQMHNIEAN KIDSGKLGYS ITVAEPDFTA AVYWIKTYQL PPRPRVEIAQ MFPADSLVSS PRAEKARLY SAIEQRLEQS LQTMEGVLSA RVHISYDIDA GENGRPPKPV HLSALAVYER GSPLAHQISD IKRFLKNSFA D VDYDNISV ...String: CKDKDLLKGL DQEQANEVIA VLQMHNIEAN KIDSGKLGYS ITVAEPDFTA AVYWIKTYQL PPRPRVEIAQ MFPADSLVSS PRAEKARLY SAIEQRLEQS LQTMEGVLSA RVHISYDIDA GENGRPPKPV HLSALAVYER GSPLAHQISD IKRFLKNSFA D VDYDNISV VLSERSDAQL QAPGTPVKRN SFATSWIVLI ILLSVMSAGF GVWYYKNHYA RNKKGITADD KAKSSNE UniProtKB: Lipoprotein PrgK |
-Macromolecule #3: Protein PrgH
Macromolecule | Name: Protein PrgH / type: protein_or_peptide / ID: 3 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 30.360537 KDa |
Sequence | String: SAKKNEPRFK NGIVAALAGF FILGIGTVGT LWILNSPQRQ AAELDSLLGQ EKERFQVLPG RDKMLYVAAQ NERDTLWARQ VLARGDYDK NARVINENEE NKRISIWLDT YYPQLAYYRI HFDEPRKPVF WLSRQRNTMS KKELEVLSQK LRALMPYADS V NITLMDDV ...String: SAKKNEPRFK NGIVAALAGF FILGIGTVGT LWILNSPQRQ AAELDSLLGQ EKERFQVLPG RDKMLYVAAQ NERDTLWARQ VLARGDYDK NARVINENEE NKRISIWLDT YYPQLAYYRI HFDEPRKPVF WLSRQRNTMS KKELEVLSQK LRALMPYADS V NITLMDDV TAAGQAEAGL KQQALPYSRR NHKGGVTFVI QGALDDVEIL RARQFVDSYY RTWGGRYVQF AIELKDDWLK GR SFQYGAE GYIKMSPGHW YFPSPL UniProtKB: Protein PrgH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: Gatan GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 2515 / Average exposure time: 0.375 sec. / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.2 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 29240 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000 |
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
-Atomic model buiding 1
Details | Initial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-5tcr: |