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- EMDB-12192: Salmonella export gate and rod refined in focussed C1 map -

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Basic information

Entry
Database: EMDB / ID: EMD-12192
TitleSalmonella export gate and rod refined in focussed C1 map
Map datapost processed volume
Sample
  • Complex: Flagellar LP ring
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar basal-body rod protein FlgG
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
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod FlgG / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G ...Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod FlgG / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / Flagellar basal-body/hook protein, C-terminal domain / FliP family / Flagellar basal body rod FlgEFG protein C-terminal / Flagella transport protein fliP family signature 2.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliQ / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgG / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria) / Salmonella typhi (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJohnson S / Furlong E / Lea SM
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust219477 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust201536 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: 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
DepositionJan 12, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7bin
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12192.png

Downloads & links

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Map

FileDownload / File: emd_12192.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost processed volume
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 768 pix.
= 638.976 Å		0.83 Å/pix.
x 768 pix.
= 638.976 Å		0.83 Å/pix.
x 768 pix.
= 638.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.017
Minimum - Maximum-0.038260378 - 0.057647962
Average (Standard dev.)3.6229252e-05 (±0.0010596468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 638.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z638.976638.976638.976
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS768768768
D min/max/mean-0.0380.0580.000

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Supplemental data

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Mask #1

Fileemd_12192_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: refinement volume

Fileemd_12192_additional_1.map
Annotationrefinement volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_12192_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_12192_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagellar LP ring

EntireName: Flagellar LP ring
Components
  • Complex: Flagellar LP ring
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar basal-body rod protein FlgG

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Supramolecule #1: Flagellar LP ring

SupramoleculeName: Flagellar LP ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)

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Macromolecule #1: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhi (bacteria)
Molecular weightTheoretical: 26.801086 KDa
SequenceString: 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

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Macromolecule #2: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Molecular weightTheoretical: 28.938865 KDa
SequenceString: 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

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Macromolecule #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Molecular weightTheoretical: 9.606758 KDa
SequenceString:
MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG

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Macromolecule #4: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 11.087662 KDa
SequenceString:
MAAIQGIEGV ISQLQATAMA ARGQDTHSQS TVSFAGQLHA ALDRISDRQA AARVQAEKFT LGEPGIALND VMADMQKASV SMQMGIQVR NKLVAAYQEV MSMQV

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Macromolecule #5: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 15.145061 KDa
SequenceString:
MLDRLDAALR FQQEALNLRA QRQEILAANI ANADTPGYQA RDIDFASELK KVMVRGREET GGVALTLTSS HHIPAQAVSS PAVDLLYRV PDQPSLDGNT VDMDRERTQF ADNSLKYQMG LTVLGSQLKG MMNVLQGGN

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Macromolecule #6: Flagellar basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 13.991889 KDa
SequenceString:
MALLNIFDIA GSALAAQSKR LNVAASNLAN ADSVTGPDGQ PYRAKQVVFQ VDAAPGQATG GVKVASVIES QAPEKLVYEP GNPLADANG YVKMPNVDVV GEMVNTMSAS RSYQANIEVL NTVKSMMLKT LTLGQ

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Macromolecule #7: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 7 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 26.121223 KDa
SequenceString: 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

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Macromolecule #8: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 8 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 27.784807 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: SIMPLE (ver. 3.0)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 60497
FSC plot (resolution estimation)

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