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- EMDB-9974: Structure of Salmonella flagellar hook reveals intermolecular dom... -

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Basic information

Entry
Database: EMDB / ID: EMD-9974
TitleStructure of Salmonella flagellar hook reveals intermolecular domain interactions for the universal joint function
Map data
Sample
  • Complex: Flagellar hook
    • Protein or peptide: Flagellar hook protein FlgE
KeywordsFlgE / universal joint / axial structure / motor protein
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytosol
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal ...Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHorvath P / Kato T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25000013 Japan
Japan Society for the Promotion of Science18K06155 Japan
CitationJournal: Biomolecules / Year: 2019
Title: Structure of Flagellar Hook Reveals Intermolecular Domain Interactions for the Universal Joint Function.
Authors: Péter Horváth / Takayuki Kato / Tomoko Miyata / Keiichi Namba /
Abstract: The bacterial flagellum is a motility organelle consisting of a rotary motor and a long helical filament as a propeller. The flagellar hook is a flexible universal joint that transmits motor torque ...The bacterial flagellum is a motility organelle consisting of a rotary motor and a long helical filament as a propeller. The flagellar hook is a flexible universal joint that transmits motor torque to the filament in its various orientations that change dynamically between swimming and tumbling of the cell upon switching the motor rotation for chemotaxis. Although the structures of the hook and hook protein FlgE from different bacterial species have been studied, the structure of hook, which has been studied most over the years, has not been solved at a high enough resolution to allow building an atomic model of entire FlgE for understanding the mechanisms of self-assembly, stability and the universal joint function. Here we report the structure of polyhook at 4.1 Å resolution by electron cryomicroscopy and helical image analysis. The density map clearly revealed folding of the entire FlgE chain forming the three domains D0, D1 and D2 and allowed us to build an atomic model. The model includes domain Dc with a long β-hairpin structure that connects domains D0 and D1 and contributes to the structural stability of the hook while allowing the flexible bending of the hook as a molecular universal joint.
History
DepositionJul 8, 2019-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 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: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kfk
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6kfk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9974.png

Downloads & links

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Map

FileDownload / File: emd_9974.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 392 pix.
= 321.44 Å		0.82 Å/pix.
x 392 pix.
= 321.44 Å		0.82 Å/pix.
x 392 pix.
= 321.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.085525736 - 0.14024903
Average (Standard dev.)0.00039747966 (±0.009452366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-196-196-392
Dimensions392392392
Spacing392392392
CellA=B=C: 321.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z392392392
origin x/y/z0.0000.0000.000
length x/y/z321.440321.440321.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-196-196-392
NC/NR/NS392392392
D min/max/mean-0.0860.1400.000

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Supplemental data

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Sample components

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Entire : Flagellar hook

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

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Supramolecule #1: Flagellar hook

SupramoleculeName: Flagellar hook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 42 kDa/nm

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Macromolecule #1: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
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
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3TRIS
100.0 mMNaClSodium Chloride
GridModel: Quantifoil R0.6/1 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 275.15 K

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Number real images: 486 / Average exposure time: 6.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal magnification: 50000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.05 Å
Applied symmetry - Helical parameters - Δ&Phi: 64.78 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 41568
Segment selectionNumber selected: 42293
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)

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Atomic model buiding 1

Initial model
PDB IDChain

3a69

chain_id: A, residue_range: 1-402, source_name: PDB, initial_model_type: experimental model

5jxl

chain_id: A, residue_range: 28-46, source_name: PDB, initial_model_type: experimental model

5jxl

chain_id: A, residue_range: 65-92, source_name: PDB, initial_model_type: experimental model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-6kfk:
Structure of Salmonella flagellar hook reveals intermolecular domain interactions for the universal joint function

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