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- EMDB-37600: Cryo-EM structure of the distal rod-hook within the flagellar mot... -

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Basic information

Entry
Database: EMDB / ID: EMD-37600
TitleCryo-EM structure of the distal rod-hook within the flagellar motor-hook complex in the CW state.
Map dataDistal rod-hook
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar basal-body rod protein FlgG
KeywordsFlagellum / Flagellar motor / Rod / Hook / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar basal-body rod FlgG / 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 FlgG / 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 basal-body rod protein FlgG
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 distal rod-hook within the flagellar motor-hook complex in the CW state.
Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ
History
DepositionSep 27, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37600.png

Downloads & links

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Map

FileDownload / File: emd_37600.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDistal rod-hook
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å		1.2 Å/pix.
x 512 pix.
= 614.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.2632293 - 1.7711838
Average (Standard dev.)-0.0019895467 (±0.082679346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 614.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_37600_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_37600_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 CW state

EntireName: C ring-containing flagellar motor-hook complex in the CW state
Components
  • Complex: C ring-containing flagellar motor-hook complex in the CW state
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar basal-body rod protein FlgG

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

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CW 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 hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 29 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 42.233152 KDa
SequenceString: MSFSQAVSGL NAAATNLDVI GNNIANSATY GFKSGTASFA DMFAGSKVGL GVKVAGITQD FTDGTTTNTG RGLDVAISQN GFFRLVDSN GSVFYSRNGQ FKLDENRNLV NMQGMQLTGY PATGTPPTIQ QGANPAPITI PNTLMAAKST TTASMQINLN S TDPVPSKT ...String:
MSFSQAVSGL NAAATNLDVI GNNIANSATY GFKSGTASFA DMFAGSKVGL GVKVAGITQD FTDGTTTNTG RGLDVAISQN GFFRLVDSN GSVFYSRNGQ FKLDENRNLV NMQGMQLTGY PATGTPPTIQ QGANPAPITI PNTLMAAKST TTASMQINLN S TDPVPSKT PFSVSDADSY NKKGTVTVYD SQGNAHDMNV YFVKTKDNEW AVYTHDSSDP AATAPTTAST TLKFNENGIL ES GGTVNIT TGTINGATAA TFSLSFLNSM QQNTGANNIV ATNQNGYKPG DLVSYQINND GTVVGNYSNE QEQVLGQIVL ANF ANNEGL ASQGDNVWAA TQASGVALLG TAGSGNFGKL TNGALEASNV DLSKELVNMI VAQRNYQSNA QTIKTQDQIL NTLV NLR

UniProtKB: Flagellar hook protein FlgE

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Macromolecule #2: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 27.784807 KDa
SequenceString: MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV ...String:
MISSLWIAKT GLDAQQTNMD VIANNLANVS TNGFKRQRAV FEDLLYQTIR QPGAQSSEQT TLPSGLQIGT GVRPVATERL HSQGNLSQT NNSKDVAIKG QGFFQVMLPD GTSAYTRDGS FQVDQNGQLV TAGGFQVQPA ITIPANALSI TIGRDGVVSV T QQGQAAPV QVGQLNLTTF MNDTGLESIG ENLYIETQSS GAPNESTPGL NGAGLLYQGY VETSNVNVAE ELVNMIQVQR AY EINSKAV STTDQMLQKL TQL

UniProtKB: Flagellar basal-body rod protein FlgG

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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
11.7 mMTris-HCltris(hydroxymethyl)aminomethane hydrochloride
4.17 mMEDTAethylenediaminetetraacetic acid
0.083 %TX-100octylphenol ethoxylate
25.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2.
DetailsThis sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 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: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46058 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 24190
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model-Angelo
SoftwareName: Coot (ver. 0.9.8.7)
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8wki:
Cryo-EM structure of the distal rod-hook within the flagellar motor-hook complex in the CW state.

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