+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12192 | |||||||||||||||
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Title | Salmonella export gate and rod refined in focussed C1 map | |||||||||||||||
Map data | post processed volume | |||||||||||||||
Sample |
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Keywords | bacterial flagellum rod bacterial flagellum export gate basal body / PROTEIN TRANSPORT | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting ...bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting / membrane => GO:0016020 / structural molecule activity / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi (bacteria) / Salmonella typhi (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Johnson S / Furlong E | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nat Microbiol / Year: 2021 Title: Molecular structure of the intact bacterial flagellar basal body. Authors: Steven Johnson / Emily J Furlong / Justin C Deme / Ashley L Nord / Joseph J E Caesar / Fabienne F V Chevance / Richard M Berry / Kelly T Hughes / Susan M Lea / Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the ...The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids. Here, we present structures of the intact Salmonella flagellar basal body, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine. | |||||||||||||||
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_12192.map.gz | 92.8 MB | EMDB map data format | |
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Header (meta data) | emd-12192-v30.xml emd-12192.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12192_fsc.xml | 27 KB | Display | FSC data file |
Images | emd_12192.png | 24.1 KB | ||
Masks | emd_12192_msk_1.map | 1.7 GB | Mask map | |
Filedesc metadata | emd-12192.cif.gz | 6.3 KB | ||
Others | emd_12192_additional_1.map.gz emd_12192_half_map_1.map.gz emd_12192_half_map_2.map.gz | 1.4 GB 1.4 GB 1.4 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12192 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12192 | HTTPS FTP |
-Validation report
Summary document | emd_12192_validation.pdf.gz | 908.1 KB | Display | EMDB validaton report |
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Full document | emd_12192_full_validation.pdf.gz | 907.7 KB | Display | |
Data in XML | emd_12192_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | emd_12192_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12192 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12192 | HTTPS FTP |
-Related structure data
Related structure data | 7binMC 7bglC 7bhqC 7bj2C 7bk0C 7nvgC 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_12192.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | post processed volume | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 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_12192_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refinement volume
File | emd_12192_additional_1.map | ||||||||||||
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Annotation | refinement volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_12192_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_12192_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Flagellar LP ring
Entire | Name: Flagellar LP ring |
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Components |
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-Supramolecule #1: Flagellar LP ring
Supramolecule | Name: Flagellar LP ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) |
-Macromolecule #1: Flagellar biosynthetic protein FliP
Macromolecule | Name: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhi (bacteria) |
Molecular weight | Theoretical: 26.801086 KDa |
Sequence | String: MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ...String: MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ILLPAYVTSE LKTAFQIGFT IFIPFLIIDL VIASVLMALG MMMVPPATIA LPFKLMLFVL VDGWQLLMGS LA QSFYS UniProtKB: Flagellar biosynthetic protein FliP |
-Macromolecule #2: Flagellar biosynthetic protein FliR
Macromolecule | Name: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) |
Molecular weight | Theoretical: 28.938865 KDa |
Sequence | String: MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA ...String: MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA FMALARAGGL IFLNGLMLAL PVITLLLTLN LALGLLNRMA PQLSIFVIGF PLTLTVGIML MAALMPLIAP FC EHLFSEI FNLLADIVSE MPINNNP UniProtKB: Flagellar biosynthetic protein FliR |
-Macromolecule #3: Flagellar biosynthetic protein FliQ
Macromolecule | Name: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) |
Molecular weight | Theoretical: 9.606758 KDa |
Sequence | String: MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG UniProtKB: Flagellar biosynthetic protein FliQ |
-Macromolecule #4: Flagellar hook-basal body complex protein FliE
Macromolecule | Name: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 11.087662 KDa |
Sequence | String: MAAIQGIEGV ISQLQATAMA ARGQDTHSQS TVSFAGQLHA ALDRISDRQA AARVQAEKFT LGEPGIALND VMADMQKASV SMQMGIQVR NKLVAAYQEV MSMQV UniProtKB: Flagellar hook-basal body complex protein FliE |
-Macromolecule #5: Flagellar basal body rod protein FlgB
Macromolecule | Name: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 15.145061 KDa |
Sequence | String: MLDRLDAALR FQQEALNLRA QRQEILAANI ANADTPGYQA RDIDFASELK KVMVRGREET GGVALTLTSS HHIPAQAVSS PAVDLLYRV PDQPSLDGNT VDMDRERTQF ADNSLKYQMG LTVLGSQLKG MMNVLQGGN UniProtKB: Flagellar basal body rod protein FlgB |
-Macromolecule #6: Flagellar basal-body rod protein FlgC
Macromolecule | Name: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 13.991889 KDa |
Sequence | String: MALLNIFDIA GSALAAQSKR LNVAASNLAN ADSVTGPDGQ PYRAKQVVFQ VDAAPGQATG GVKVASVIES QAPEKLVYEP GNPLADANG YVKMPNVDVV GEMVNTMSAS RSYQANIEVL NTVKSMMLKT LTLGQ UniProtKB: Flagellar basal-body rod protein FlgC |
-Macromolecule #7: Flagellar basal-body rod protein FlgF
Macromolecule | Name: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 7 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 26.121223 KDa |
Sequence | String: MDHAIYTAMG AASQTLNQQA VTASNLANAS TPGFRAQLNA LRAVPVDGLS LATRTLVTAS TPGADMTPGQ LDYTSRPLDV ALQQDGWLV VQAADGAEGY TRNGNIQVGP TGQLTIQGHP VIGEGGPITV PEGSEITIAA DGTISALNPG DPPNTVAPVG R LKLVKAEG ...String: MDHAIYTAMG AASQTLNQQA VTASNLANAS TPGFRAQLNA LRAVPVDGLS LATRTLVTAS TPGADMTPGQ LDYTSRPLDV ALQQDGWLV VQAADGAEGY TRNGNIQVGP TGQLTIQGHP VIGEGGPITV PEGSEITIAA DGTISALNPG DPPNTVAPVG R LKLVKAEG NEVQRSDDGL FRLTAEAQAE RGAVLAADPS IRIMSGVLEG SNVKPVEAMT DMIANARRFE MQMKVITSVD EN EGRANQL LSMS UniProtKB: Flagellar basal-body rod protein FlgF |
-Macromolecule #8: Flagellar basal-body rod protein FlgG
Macromolecule | Name: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 8 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 |
Molecular weight | Theoretical: 27.784807 KDa |
Sequence | String: MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV ...String: MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV QVGQLNLTTF MNDTGLESIG ENLYIETQSS GAPNESTPGL NGAGLLYQGY VETSNVNVAE ELVNMIQVQR AY EINSKAV STTDQMLQKL TQL UniProtKB: Flagellar basal-body rod protein FlgG |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 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 |