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- EMDB-30348: Cryo-EM structure of the flagellar proximal rod with FliF peptide... -

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Basic information

Entry
Database: EMDB / ID: EMD-30348
TitleCryo-EM structure of the flagellar proximal rod with FliF peptides from Salmonella
Map dataDensity map of the flagellar proximal rod
Sample
  • Complex: Flagellar motor-hook complex
    • Protein or peptide: Flagellar MS ring L2
    • Protein or peptide: Flagellar MS ring L1
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal body rod protein FlgB
KeywordsProximal rod / FlgC / FlgB / FliF / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / plasma membrane
Similarity search - Function
Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal ...Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / 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 basal-body rod protein FlgC / Flagellar M-ring protein / Flagellar basal body rod protein FlgB
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTan JX / Chang SH
Funding support China, 6 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504803 China
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81501717 China
CitationJournal: Cell / Year: 2021
Title: Structural basis of assembly and torque transmission of the bacterial flagellar motor.
Authors: Jiaxing Tan / Xing Zhang / Xiaofei Wang / Caihuang Xu / Shenghai Chang / Hangjun Wu / Ting Wang / Huihui Liang / Haichun Gao / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key ...The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key determinant of pathogenicity. The detailed structure of the flagellar motor remains unknown. Here we present an atomic-resolution cryoelectron microscopy (cryo-EM) structure of the bacterial flagellar motor complexed with the hook, consisting of 175 subunits with a molecular mass of approximately 6.3 MDa. The structure reveals that 10 peptides protruding from the MS ring with the FlgB and FliE subunits mediate torque transmission from the MS ring to the rod and overcome the symmetry mismatch between the rotational and helical structures in the motor. The LP ring contacts the distal rod and applies electrostatic forces to support its rotation and torque transmission to the hook. This work provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the flagellar motor.
History
DepositionJun 30, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.644
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.644
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cg0
  • Surface level: 0.544
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cg0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30348.png

Downloads & links

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Map

FileDownload / File: emd_30348.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of the flagellar proximal rod
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 512 pix.
= 669.184 Å		1.31 Å/pix.
x 512 pix.
= 669.184 Å		1.31 Å/pix.
x 512 pix.
= 669.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.644 / Movie #1: 0.644
Minimum - Maximum-1.2291619 - 3.0922384
Average (Standard dev.)0.001921918 (±0.066367894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 669.184 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z669.184669.184669.184
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2293.0920.002

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Supplemental data

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Sample components

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Entire : Flagellar motor-hook complex

EntireName: Flagellar motor-hook complex
Components
  • Complex: Flagellar motor-hook complex
    • Protein or peptide: Flagellar MS ring L2
    • Protein or peptide: Flagellar MS ring L1
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal body rod protein FlgB

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Supramolecule #1: Flagellar motor-hook complex

SupramoleculeName: Flagellar motor-hook complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Macromolecule #1: Flagellar MS ring L2

MacromoleculeName: Flagellar MS ring L2 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 1.294587 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #2: Flagellar MS ring L1

MacromoleculeName: Flagellar MS ring L1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 1.998195 KDa
SequenceString:
GVPGALSNQP APPNEAPIAT P

UniProtKB: Flagellar M-ring protein

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Macromolecule #3: Flagellar basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 13.991889 KDa
SequenceString:
MALLNIFDIA GSALAAQSKR LNVAASNLAN ADSVTGPDGQ PYRAKQVVFQ VDAAPGQATG GVKVASVIES QAPEKLVYEP GNPLADANG YVKMPNVDVV GEMVNTMSAS RSYQANIEVL NTVKSMMLKT LTLGQ

UniProtKB: Flagellar basal-body rod protein FlgC

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Macromolecule #4: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 6 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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