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- EMDB-30335: Cryo-EM structure of the flagellar LP ring from Salmonella -

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Basic information

Entry
Database: EMDB / ID: EMD-30335
TitleCryo-EM structure of the flagellar LP ring from Salmonella
Map dataFlagellar LP ring from Salmonella
Sample
  • Complex: Flagellar hook-basal body
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
  • Ligand: OCTANOIC ACID (CAPRYLIC ACID)
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTan JX / Chang SH / Wang XF / Xu CH / Zhou Y / Zhang X / Zhu YQ
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 12, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.81
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.81
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cbl
  • Surface level: 0.81
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cbl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30335.png

Downloads & links

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Map

FileDownload / File: emd_30335.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlagellar LP ring from Salmonella
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.809 / Movie #1: 0.81
Minimum - Maximum-3.0397234 - 6.407339
Average (Standard dev.)0.0022116848 (±0.09231284)
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-3.0406.4070.002

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Supplemental data

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Sample components

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Entire : Flagellar hook-basal body

EntireName: Flagellar hook-basal body
Components
  • Complex: Flagellar hook-basal body
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
  • Ligand: OCTANOIC ACID (CAPRYLIC ACID)

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Supramolecule #1: Flagellar hook-basal body

SupramoleculeName: Flagellar hook-basal body / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Macromolecule #1: Flagellar L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 24.726666 KDa
SequenceString: MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ ...String:
MQKYALHAYP VMALMVATLT GCAWIPAKPL VQGATTAQPI PGPVPVANGS IFQSAQPINY GYQPLFEDRR PRNIGDTLTI VLQENVSAS KSSSANASRD GKTSFGFDTV PRYLQGLFGN SRADMEASGG NSFNGKGGAN ASNTFSGTLT VTVDQVLANG N LHVVGEKQ IAINQGTEFI RFSGVVNPRT ISGSNSVPST QVADARIEYV GNGYINEAQN MGWLQRFFLN LSPM

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Macromolecule #2: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 38.194176 KDa
SequenceString: MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG ...String:
MFKALAGIVL ALVATLAHAE RIRDLTSVQG VRENSLIGYG LVVGLDGTGD QTTQTPFTTQ TLNNMLSQLG ITVPTGTNMQ LKNVAAVMV TASYPPFARQ GQTIDVVVSS MGNAKSLRGG TLLMTPLKGV DSQVYALAQG NILVGGAGAS AGGSSVQVNQ L NGGRITNG AIIERELPTQ FGAGNTINLQ LNDEDFTMAQ QITDAINRAR GYGSATALDA RTVQVRVPSG NSSQVRFLAD IQ NMEVNVT PQDAKVVINS RTGSVVMNRE VTLDSCAVAQ GNLSVTVNRQ LNVNQPNTPF GGGQTVVTPQ TQIDLRQSGG SLQ SVRSSA NLNSVVRALN ALGATPMDLM SILQSMQSAG CLRAKLEII

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Macromolecule #3: OCTANOIC ACID (CAPRYLIC ACID)

MacromoleculeName: OCTANOIC ACID (CAPRYLIC ACID) / type: ligand / ID: 3 / Number of copies: 26 / Formula: OCA
Molecular weightTheoretical: 144.211 Da
Chemical component information

ChemComp-OCA:
OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid

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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
10.0 mMTris-HClTristris(hydroxymethyl)aminomethane hydrochloride-hydrochloride
5.0 mMEDTAEthylenediaminetetraacetic acidethylene diamine tetraacetic acid
0.1 %TX-100octylphenol ethoxylate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80548

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7cbl:
Cryo-EM structure of the flagellar LP ring from Salmonella

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