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- EMDB-9909: Salmonella hook in curved state - unsymmetrized cryo-EM map -

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Basic information

Entry
Database: EMDB / ID: EMD-9909
TitleSalmonella hook in curved state - unsymmetrized cryo-EM map
Map datafull map
Sample
  • Complex: Bacterial flagellar polyhook
    • Protein or peptide: Flagellar hook protein FlgE
Keywordsbacterial / hook / flexible joint / flagella / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsShibata S / Matsunami H
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of Science17K17085 Japan
Japan Society for the Promotion of Science19K10083 Japan
Japan Society for the Promotion of Science17K07318 Japan
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Torque transmission mechanism of the curved bacterial flagellar hook revealed by cryo-EM.
Authors: Satoshi Shibata / Hideyuki Matsunami / Shin-Ichi Aizawa / Matthias Wolf /
Abstract: Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, ...Bacterial locomotion by rotating flagella is achieved through the hook, which transmits torque from the motor to the filament. The hook is a tubular structure composed of a single type of protein, yet it adopts a curved shape. To perform its function, it must be simultaneously flexible and torsionally rigid. The molecular mechanism by which chemically identical subunits form such a dynamic structure is unknown. Here, we show the complete structure of the hook from Salmonella enterica in its supercoiled 'curved' state, at 2.9 Å resolution. Subunits in the curved hook are grouped into 11 distinctive conformations, each shared along 11 protofilaments. The domains of the elongated hook subunit behave as rigid bodies connected by two hinge regions. The reconstituted model demonstrates how identical subunits can dynamically change conformation by physical interactions while bending. These multiple subunit states contradict the two-state model, which is a key feature of flagellar polymorphism.
History
DepositionMay 19, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k3i
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6k3i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9909.png

Downloads & links

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Map

FileDownload / File: emd_9909.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 384 pix.
= 533.76 Å		1.39 Å/pix.
x 384 pix.
= 533.76 Å		1.39 Å/pix.
x 384 pix.
= 533.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-9.643155999999999 - 14.196548
Average (Standard dev.)-0.00000000214617 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 533.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z533.760533.760533.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-9.64314.197-0.000

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Supplemental data

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Half map: half map 1

Fileemd_9909_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_9909_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacterial flagellar polyhook

EntireName: Bacterial flagellar polyhook
Components
  • Complex: Bacterial flagellar polyhook
    • Protein or peptide: Flagellar hook protein FlgE

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Supramolecule #1: Bacterial flagellar polyhook

SupramoleculeName: Bacterial flagellar polyhook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 2.8 MDa

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Macromolecule #1: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 66 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 42.101957 KDa
SequenceString: SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP ...String:
SFSQAVSGLN AAATNLDVIG NNIANSATYG FKSGTASFAD MFAGSKVGLG VKVAGITQDF TDGTTTNTGR GLDVAISQNG FFRLVDSNG SVFYSRNGQF KLDENRNLVN MQGMQLTGYP ATGTPPTIQQ GANPAPITIP NTLMAAKSTT TASMQINLNS T DPVPSKTP FSVSDADSYN KKGTVTVYDS QGNAHDMNVY FVKTKDNEWA VYTHDSSDPA ATAPTTASTT LKFNENGILE SG GTVNITT GTINGATAAT FSLSFLNSMQ QNTGANNIVA TNQNGYKPGD LVSYQINNDG TVVGNYSNEQ EQVLGQIVLA NFA NNEGLA SQGDNVWAAT QASGVALLGT AGSGNFGKLT NGALEASNVD LSKELVNMIV AQRNYQSNAQ TIKTQDQILN TLVN LR

UniProtKB: Flagellar hook protein FlgE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 3.5 / Component - Concentration: 50.0 mM / Component - Formula: C2H5NO2 / Component - Name: Glycine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 4.0uL.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.13 µm / Calibrated defocus min: 0.43 µm / Calibrated magnification: 107914 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.13 µm / Nominal defocus min: 0.43 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 100.0 K
Detailsnanoprobe, parallel beam illumination
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 2655 / Average exposure time: 2.0 sec. / Average electron dose: 89.0 e/Å2
Details: frame alignment and dose weighting using motioncor2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 998061
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1wlg

Initial angle assignmentType: OTHER / Software - Name: cisTEM (ver. 1.0.1-beta)
Details: global search with cisTEM using a synthetic superhelical tube
Final 3D classificationNumber classes: 3 / Avg.num./class: 78179 / Software - Name: cisTEM (ver. 1.0.1-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.1-beta) / Details: cisTEM refinement with likelihood blurring
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.1-beta) / Number images used: 234536
Detailsframe alignment and integration with motioncor2 incl. dose weighting
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1wlg


Chain - Chain ID: A / Chain - Residue range: 70-359 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: CC
Output model

PDB-6k3i:
Salmonella hook in curved state - 66 subunit models

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