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- EMDB-37595: Cryo-EM structure of the MS ring with FlgB and FliE within the fl... -

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Basic information

Entry
Database: EMDB / ID: EMD-37595
TitleCryo-EM structure of the MS ring with FlgB and FliE within the flagellar motor-hook complex in the CW state.
Map dataMS ring with FlgB-Dc loops and FliE
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar M-ring protein
KeywordsFlagellum / Flagellar motor / MS ring / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal ...Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar M-ring protein / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTan JX / Zhang L / Zhou Y / Zhu YQ
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the MS ring with FlgB and FliE within the flagellar motor-hook complex in the CW state.
Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ
History
DepositionSep 27, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37595.png

Downloads & links

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Map

FileDownload / File: emd_37595.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMS ring with FlgB-Dc loops and FliE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.71194994 - 1.1748688
Average (Standard dev.)-0.0014819838 (±0.045935895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 614.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_37595_half_map_1.map
AnnotationHalf map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_37595_half_map_2.map
AnnotationHalf map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C ring-containing flagellar motor-hook complex in the CW state

EntireName: C ring-containing flagellar motor-hook complex in the CW state
Components
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar M-ring protein

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Supramolecule #1: C ring-containing flagellar motor-hook complex in the CW state

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CW state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

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Macromolecule #1: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 11.087662 KDa
SequenceString:
MAAIQGIEGV ISQLQATAMA ARGQDTHSQS TVSFAGQLHA ALDRISDRQA AARVQAEKFT LGEPGIALND VMADMQKASV SMQMGIQVR NKLVAAYQEV MSMQV

UniProtKB: Flagellar hook-basal body complex protein FliE

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Macromolecule #2: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 15.145061 KDa
SequenceString:
MLDRLDAALR FQQEALNLRA QRQEILAANI ANADTPGYQA RDIDFASELK KVMVRGREET GGVALTLTSS HHIPAQAVSS PAVDLLYRV PDQPSLDGNT VDMDRERTQF ADNSLKYQMG LTVLGSQLKG MMNVLQGGN

UniProtKB: Flagellar basal body rod protein FlgB

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Macromolecule #3: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 3 / Number of copies: 34 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 61.295645 KDa
SequenceString: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String:
MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE

UniProtKB: Flagellar M-ring protein

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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
Component:
ConcentrationFormulaName
11.7 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
4.17 mMEDTAethylenediaminetetraacetic acid
0.083 % v/vTX-100octylphenol ethoxylate
25.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2.
DetailsThis sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46058 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 24190
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model-Angelo
SoftwareName: UCSF Chimera (ver. 1.17)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8wk4:
Cryo-EM structure of the MS ring with FlgB and FliE within the flagellar motor-hook complex in the CW state.

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