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- EMDB-60959: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60959
TitleSalmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
Map data
Sample
  • Complex: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
    • Protein or peptide: Flagellin
Keywordsflagellin / tail / flagella / filament / MOTOR PROTEIN
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / receptor ligand activity / structural molecule activity / extracellular space
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsWaraich K / Makino F / Miyata T / Kinoshita M / Minamino T / Namba K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: To Be Published
Title: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
Authors: Waraich K / Makino F / Miyata T / Kinoshita M / Minamino T / Namba K
History
DepositionJul 25, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60959.png

Downloads & links

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Map

FileDownload / File: emd_60959.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.8434795 - 1.5907743
Average (Standard dev.)0.012149658 (±0.11406497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60959_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60959_half_map_2.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 : Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)...

EntireName: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
Components
  • Complex: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
    • Protein or peptide: Flagellin

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Supramolecule #1: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292)...

SupramoleculeName: Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament
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: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 42.587551 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
SequenceString: AQVINTNSLS LLTQNNLNKS QSALGTAIER LSSGLRINSA KDDAAGQAIA NRFTANIKGL TQASRNANDG ISIAQTTEGA LNEINNNLQ RVRELAVQSA NSTNSQSDLD SIQAEITQRL NEIDRVSGQT QFNGVKVLAQ DNTLTIQVGA NDGETIDIDL K QINSQTLG ...String:
AQVINTNSLS LLTQNNLNKS QSALGTAIER LSSGLRINSA KDDAAGQAIA NRFTANIKGL TQASRNANDG ISIAQTTEGA LNEINNNLQ RVRELAVQSA NSTNSQSDLD SIQAEITQRL NEIDRVSGQT QFNGVKVLAQ DNTLTIQVGA NDGETIDIDL K QINSQTLG LDTLNVQQKY KVSDTAATVT GYADTTIALD NSTFKAALTA AGVTGTASVV KMSYTDNNGK TIDGGLAVKV GD DYYSATQ NKDGSISINT TKYTADDGTS KTALNKLGGA DGKTEVVSIG GKTYAASKAE GHNFKAQPDL AEAAATTTEN PLQ KIDAAL AQVDTLRSDL AAVQNRFNSA ITNLGNTVNN LTSARSRIED SDYATEVSNM SRAQILQQAG TSVLAQANQV PQNV LSLLR

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloride
25.0 mMTrisTris(hydroxymethyl)aminomethane
1.0 mMEDTAethylenediaminetetraacetic acid
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 40.0 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: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsHelical processing using cryosparc.
Final reconstructionApplied symmetry - Helical parameters - Δz: 65.305 Å
Applied symmetry - Helical parameters - Δ&Phi: 4.801 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 726742
Segment selectionNumber selected: 726742
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3a5x


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: 3A5X
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9iwq:
Salmonella enterica serovar Typhimurium FliC(G426A)delta(204-292) forming the L-type straight filament

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