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- EMDB-37618: Cryo-EM structure of the LP ring within the flagellar motor-hook ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37618
TitleCryo-EM structure of the LP ring within the flagellar motor-hook complex in the CCW state.
Map dataExperimental map
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CCW state
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
KeywordsFlagellum / Flagellar motor / LP ring / MOTOR 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 L-ring protein / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 LP ring within the flagellar motor-hook complex in the CCW state.
Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ
History
DepositionSep 29, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37618.png

Downloads & links

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Map

FileDownload / File: emd_37618.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationExperimental map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-5.415996 - 5.866306
Average (Standard dev.)-0.003844901 (±0.19107969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 681.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_37618_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_37618_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 CCW state

EntireName: C ring-containing flagellar motor-hook complex in the CCW state
Components
  • Complex: C ring-containing flagellar motor-hook complex in the CCW state
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein

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

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CCW 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 L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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

UniProtKB: Flagellar L-ring protein

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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 enterica subsp. enterica serovar Typhimurium str. LT2 (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

UniProtKB: Flagellar P-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
10.0 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
5.0 mMEDTAethylenediaminetetraacetic acid
0.1 %TX-100octylphenol ethoxylate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1.

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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: 45.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22192 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C26 (26 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 11858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7cbl


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8wle:
Cryo-EM structure of the LP ring within the flagellar motor-hook complex in the CCW state.

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