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- EMDB-30398: CryoEM structure of S.typhimurium flagellar LP ring -

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Basic information

Entry
Database: EMDB / ID: EMD-30398
TitleCryoEM structure of S.typhimurium flagellar LP ring
Map dataCryoEM structure of S.typhimurium flagellar LP ring
Sample
  • Complex: LP ring
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagellar L-ring protein
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 P-ring protein / Flagellar L-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Salmonella typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYamaguchi T / Makino F / Miyata T / Minamino T / Kato T / Namba K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP25000013,JP18K06155,JP26293097,JP19H03182,JP15H01640 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117,JP17pc0101020 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the molecular bushing of the bacterial flagellar motor.
Authors: Tomoko Yamaguchi / Fumiaki Makino / Tomoko Miyata / Tohru Minamino / Takayuki Kato / Keiichi Namba /
Abstract: The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable ...The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface.
History
DepositionJul 21, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: PDBj / 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
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  • Surface view with fitted model
  • Atomic models: PDB-7clr
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7clr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30398.png

Downloads & links

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Map

FileDownload / File: emd_30398.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of S.typhimurium flagellar LP ring
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 400 pix.
= 580. Å		1.45 Å/pix.
x 400 pix.
= 580. Å		1.45 Å/pix.
x 400 pix.
= 580. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.031408295 - 0.09122549
Average (Standard dev.)0.00021971043 (±0.002537645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-199-199-199
Dimensions400400400
Spacing400400400
CellA=B=C: 580.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z580.000580.000580.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-199-199-199
NC/NR/NS400400400
D min/max/mean-0.0310.0910.000

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Supplemental data

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Mask #1

Fileemd_30398_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LP ring

EntireName: LP ring
Components
  • Complex: LP ring
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagellar L-ring protein

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Supramolecule #1: LP ring

SupramoleculeName: LP ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Bushing of flagellar motor
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: HK1002

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Macromolecule #1: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (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 #2: Flagellar L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (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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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
50.0 mMC4H11NO3Tris-HCl
50.0 mMNaClSodium chloride
25.0 mMC3H4N2Imidazole
0.05 % (w/v)C47H88O22Lauryl Maltose Neopentyl Glycol(LMNG)
0.05 % (w/v)Triton X-100
Sugar embeddingMaterial: buffer
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number real images: 12759 / Average exposure time: 10.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 8.23 µm / Calibrated defocus min: 0.275 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 64418
Details: particles were picked up by YOLOPick.py (in-house python program)
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C26 (26 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta-2) / Number images used: 10802
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta-2)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.0 beta-2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 38
Output model

PDB-7clr:
CryoEM structure of S.typhimurium flagellar LP ring

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