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- EMDB-37625: Cryo-EM structure of the MS ring with export apparatus and proxim... -

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Basic information

Entry
Database: EMDB / ID: EMD-37625
TitleCryo-EM structure of the MS ring with export apparatus and proximal rod within the motor-hook complex in the CCW state
Map data
Sample
  • Complex: C ring-containing flagellar motor-hook complex in the CCW state
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC
KeywordsFlagellum / Flagellar motor / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting ...bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar basal-body rod protein FlgC / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 ...Flagellar basal-body rod protein FlgC / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / 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 biosynthetic protein FliQ / Flagellar M-ring protein / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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 MS ring with export apparatus and proximal rod within the motor-hook complex in the CCW state
Authors: Tan JX / Zhang L / Zhou Y / Zhu YQ
History
DepositionSep 30, 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_37625.png

Downloads & links

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Map

FileDownload / File: emd_37625.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å		1.33 Å/pix.
x 512 pix.
= 681.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.64231545 - 1.6891068
Average (Standard dev.)-0.0029691025 (±0.07835422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 681.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37625_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 : C ring-containing flagellar motor-hook complex in the CCW state

EntireName: C ring-containing flagellar motor-hook complex in the CCW state
Components
  • Complex: C ring-containing flagellar motor-hook complex in the CCW state
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC

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

SupramoleculeName: C ring-containing flagellar motor-hook complex in the CCW 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 M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 76 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 61.295645 KDa
SequenceString: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String:
MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE

UniProtKB: Flagellar M-ring protein

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Macromolecule #2: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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 #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 9.606758 KDa
SequenceString:
MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG

UniProtKB: Flagellar biosynthetic protein FliQ

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Macromolecule #4: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 28.938865 KDa
SequenceString: MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA ...String:
MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA FMALARAGGL IFLNGLMLAL PVITLLLTLN LALGLLNRMA PQLSIFVIGF PLTLTVGIML MAALMPLIAP FC EHLFSEI FNLLADIVSE MPINNNP

UniProtKB: Flagellar biosynthetic protein FliR

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Macromolecule #5: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 5 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 26.801086 KDa
SequenceString: MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ...String:
MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ILLPAYVTSE LKTAFQIGFT IFIPFLIIDL VIASVLMALG MMMVPPATIA LPFKLMLFVL VDGWQLLMGS LA QSFYS

UniProtKB: Flagellar biosynthetic protein FliP

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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 enterica subsp. enterica serovar Typhimurium str. LT2 (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 basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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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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
5.0 mMEDTAethylenediaminetetraacetic acid
0.1 % v/vTX-100octylphenol ethoxylate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot time: 2 Blot force: -15 Wait time: 60 Blot total: 1.

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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: 45.0 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: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22192 / Details: Particles were manually picked using cryoSPARC
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 11858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelModel-Angelo
source_name: PDB, initial_model_type: experimental model

7cgo

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8wln:
Cryo-EM structure of the MS ring with export apparatus and proximal rod within the motor-hook complex in the CCW state

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