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- EMDB-31008: Cryo-EM structure of the flagellar rod with partial hook from Sal... -

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Basic information

Entry
Database: EMDB / ID: EMD-31008
TitleCryo-EM structure of the flagellar rod with partial hook from Salmonella
Map dataRod, 3.3 angstrom
Sample
  • Complex: Flagellar motor-hook
    • Protein or peptide: Flagellar basal-body rod protein FlgG
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar MS ring L2
    • Protein or peptide: Flagellar MS ring L1
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar hook protein FlgE
KeywordsFlagella / Rod / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility ...bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / plasma membrane / cytosol
Similarity search - Function
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / 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-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / 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 / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar basal-body rod protein FlgC / Flagellar hook protein FlgE / Flagellar basal-body rod protein FlgG / Flagellar M-ring protein / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE
Similarity search - Component
Biological speciesSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTan JX / Chang SH
Funding support China, 6 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504803 China
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)81530068 China
National Natural Science Foundation of China (NSFC)81501717 China
CitationJournal: Cell / Year: 2021
Title: Structural basis of assembly and torque transmission of the bacterial flagellar motor.
Authors: Jiaxing Tan / Xing Zhang / Xiaofei Wang / Caihuang Xu / Shenghai Chang / Hangjun Wu / Ting Wang / Huihui Liang / Haichun Gao / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key ...The bacterial flagellar motor is a supramolecular protein machine that drives rotation of the flagellum for motility, which is essential for bacterial survival in different environments and a key determinant of pathogenicity. The detailed structure of the flagellar motor remains unknown. Here we present an atomic-resolution cryoelectron microscopy (cryo-EM) structure of the bacterial flagellar motor complexed with the hook, consisting of 175 subunits with a molecular mass of approximately 6.3 MDa. The structure reveals that 10 peptides protruding from the MS ring with the FlgB and FliE subunits mediate torque transmission from the MS ring to the rod and overcome the symmetry mismatch between the rotational and helical structures in the motor. The LP ring contacts the distal rod and applies electrostatic forces to support its rotation and torque transmission to the hook. This work provides detailed molecular insights into the structure, assembly, and torque transmission mechanisms of the flagellar motor.
History
DepositionFeb 28, 2021-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
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: 0.65
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e82
  • Surface level: 0.65
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31008.png

Downloads & links

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Map

FileDownload / File: emd_31008.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRod, 3.3 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 512 pix.
= 669.184 Å		1.31 Å/pix.
x 512 pix.
= 669.184 Å		1.31 Å/pix.
x 512 pix.
= 669.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65 / Movie #1: 0.65
Minimum - Maximum-1.3951496 - 2.7218342
Average (Standard dev.)-0.00016297582 (±0.07759548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 669.184 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z669.184669.184669.184
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.3952.722-0.000

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Supplemental data

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Sample components

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Entire : Flagellar motor-hook

EntireName: Flagellar motor-hook
Components
  • Complex: Flagellar motor-hook
    • Protein or peptide: Flagellar basal-body rod protein FlgG
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar MS ring L2
    • Protein or peptide: Flagellar MS ring L1
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar hook protein FlgE

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Supramolecule #1: Flagellar motor-hook

SupramoleculeName: Flagellar motor-hook / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)

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Macromolecule #1: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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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Macromolecule #2: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 26.121223 KDa
SequenceString: MDHAIYTAMG AASQTLNQQA VTASNLANAS TPGFRAQLNA LRAVPVDGLS LATRTLVTAS TPGADMTPGQ LDYTSRPLDV ALQQDGWLV VQAADGAEGY TRNGNIQVGP TGQLTIQGHP VIGEGGPITV PEGSEITIAA DGTISALNPG DPPNTVAPVG R LKLVKAEG ...String:
MDHAIYTAMG AASQTLNQQA VTASNLANAS TPGFRAQLNA LRAVPVDGLS LATRTLVTAS TPGADMTPGQ LDYTSRPLDV ALQQDGWLV VQAADGAEGY TRNGNIQVGP TGQLTIQGHP VIGEGGPITV PEGSEITIAA DGTISALNPG DPPNTVAPVG R LKLVKAEG NEVQRSDDGL FRLTAEAQAE RGAVLAADPS IRIMSGVLEG SNVKPVEAMT DMIANARRFE MQMKVITSVD EN EGRANQL LSMS

UniProtKB: Flagellar basal-body rod protein FlgF

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Macromolecule #3: Flagellar MS ring L2

MacromoleculeName: Flagellar MS ring L2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 1.294587 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: Flagellar MS ring L1

MacromoleculeName: Flagellar MS ring L1 / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 1.998195 KDa
SequenceString:
GVPGALSNQP APPNEAPIAT P

UniProtKB: Flagellar M-ring protein

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Macromolecule #5: Flagellar basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 13.991889 KDa
SequenceString:
MALLNIFDIA GSALAAQSKR LNVAASNLAN ADSVTGPDGQ PYRAKQVVFQ VDAAPGQATG GVKVASVIES QAPEKLVYEP GNPLADANG YVKMPNVDVV GEMVNTMSAS RSYQANIEVL NTVKSMMLKT LTLGQ

UniProtKB: Flagellar basal-body rod protein FlgC

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Macromolecule #6: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 6 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 15.145061 KDa
SequenceString:
MLDRLDAALR FQQEALNLRA QRQEILAANI ANADTPGYQA RDIDFASELK KVMVRGREET GGVALTLTSS HHIPAQAVSS PAVDLLYRV PDQPSLDGNT VDMDRERTQF ADNSLKYQMG LTVLGSQLKG MMNVLQGGN

UniProtKB: Flagellar basal body rod protein FlgB

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Macromolecule #7: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Molecular weightTheoretical: 11.087662 KDa
SequenceString:
MAAIQGIEGV ISQLQATAMA ARGQDTHSQS TVSFAGQLHA ALDRISDRQA AARVQAEKFT LGEPGIALND VMADMQKASV SMQMGIQVR NKLVAAYQEV MSMQV

UniProtKB: Flagellar hook-basal body complex protein FliE

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Macromolecule #8: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 8 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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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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-hydrochloride
5.0 mMEDTAethylene diamine tetraacetic acid
0.1 %TX-100octylphenol ethoxylate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 6 seconds before plunging.

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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: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102044
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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