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- EMDB-72847: LPHT-ring in Vibrio cholerae at disassembled, closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-72847
TitleLPHT-ring in Vibrio cholerae at disassembled, closed state
Map data
Sample
  • Cell: Vibrio cholerae DflhG
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagellar protein FlgT
    • Protein or peptide: Sodium-type flagellar protein MotY
    • Protein or peptide: Sodium-type flagellar protein MotX
    • Protein or peptide: Lipoprotein
KeywordsIn situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / T-ring / MotX / C26 assembled state / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / FlgT, N-terminal domain superfamily / MotY N-terminal domain / MotY N-terminal domain ...Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / FlgT, N-terminal domain superfamily / MotY N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / : / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Sodium-type flagellar protein MotX / Flagellar protein FlgT / Lipoprotein / Flagellar L-ring protein / Flagellar P-ring protein / Sodium-type flagellar protein MotY
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsGuo W / Yue J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI132818 United States
CitationJournal: To Be Published
Title: In-situ cryo-EM structures reveal mechanisms of sheathed flagellar assembly, rotation, and disassembly in Vibrio cholerae
Authors: Wangbiao G / Jian Y / Jin HP / Fitnat Y / Jun L
History
DepositionSep 24, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72847.png

Downloads & links

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Map

FileDownload / File: emd_72847.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3868437 - 0.8472436
Average (Standard dev.)0.012706139 (±0.065536745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72847_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_72847_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_72847_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_72847_half_map_2.map
Projections & Slices
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Sample components

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Entire : Vibrio cholerae DflhG

EntireName: Vibrio cholerae DflhG
Components
  • Cell: Vibrio cholerae DflhG
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagellar protein FlgT
    • Protein or peptide: Sodium-type flagellar protein MotY
    • Protein or peptide: Sodium-type flagellar protein MotX
    • Protein or peptide: Lipoprotein

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Supramolecule #1: Vibrio cholerae DflhG

SupramoleculeName: Vibrio cholerae DflhG / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

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Macromolecule #1: Flagellar L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 27.54148 KDa
SequenceString: MKRLLASSLL ILLSGCSLMQ PPIESAETIQ GTTTVDAVEG DKSESNSGLT DALRNRTDPV AGDPAWAPIH PKGKPEHYAA ETGSLFNLA SSSSMYDDSK PRGVGDIITV TLNESTKAAK SADADLNKKN DASMDPLAVG GKDLTIGDYN FSYALKNDNK F SGSAAANQ ...String:
MKRLLASSLL ILLSGCSLMQ PPIESAETIQ GTTTVDAVEG DKSESNSGLT DALRNRTDPV AGDPAWAPIH PKGKPEHYAA ETGSLFNLA SSSSMYDDSK PRGVGDIITV TLNESTKAAK SADADLNKKN DASMDPLAVG GKDLTIGDYN FSYALKNDNK F SGSAAANQ SNSMSGSITV EVIEVLANGN LVIRGEKWLT LNTGDEYIRL SGTIRPDDID FDNTIASNRI SNARIQYSGT GT NQDMQEP GFLARFFNVS L

UniProtKB: Flagellar L-ring protein

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Macromolecule #2: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 37.694059 KDa
SequenceString: MRKFTILLML LLASSAQAAR IKDVAQVAGV RNNQLVGYGL VTGLPGTGES TPFTDQSFNA MLQSFGIQLP PGTKPKTKNV AAVIVTADL PAFSKQGQTI DITVSSIGSA KSLRGGTLMQ TFLKGLDGQV YAVAQGNLVV SGFSATGADG SKIVGNNPTV G MISSGAIV ...String:
MRKFTILLML LLASSAQAAR IKDVAQVAGV RNNQLVGYGL VTGLPGTGES TPFTDQSFNA MLQSFGIQLP PGTKPKTKNV AAVIVTADL PAFSKQGQTI DITVSSIGSA KSLRGGTLMQ TFLKGLDGQV YAVAQGNLVV SGFSATGADG SKIVGNNPTV G MISSGAIV EREVPNPFGR GDYITFNLFE SDFTTAQRLA DAVNQFLGPQ MASAVDAASI KVRAPRDLSQ RVAFLSAIEN LE FNPADSA AKIIVNSRTG TIVVGQNVRL KPAAVTHGGM TVAIKENLNV SQPNALGGGQ TVVVPNTEIE VTEKQGKMFK LEP GVTLDD LVRAVNEVGA APSDLMAILQ ALKQAGAIEG QLIII

UniProtKB: Flagellar P-ring protein

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Macromolecule #3: Flagellar protein FlgT

MacromoleculeName: Flagellar protein FlgT / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 42.647734 KDa
SequenceString: MKKNILSIIS ALWMMLQLPS AHAAWYEVTG SAAIVSSEEV ARLHALEDAL YKAVNFAGAD IGSISNLMPL LESDRREYLF ANHEVRYIL IEERKAINNV MYVRTRIDIY PSATACHVEQ YKKTMLIGNI DLASPQQAVM GQIYQVGDDF AQVINRRLEQ E SRSFVSVG ...String:
MKKNILSIIS ALWMMLQLPS AHAAWYEVTG SAAIVSSEEV ARLHALEDAL YKAVNFAGAD IGSISNLMPL LESDRREYLF ANHEVRYIL IEERKAINNV MYVRTRIDIY PSATACHVEQ YKKTMLIGNI DLASPQQAVM GQIYQVGDDF AQVINRRLEQ E SRSFVSVG TTQYDIDPKA PERIKMIAQD AGAQYIMGGM ITDLTATIEQ KTLQDDIINR QFAMEISVFD GKTGNEVMTR TY REVARWP FPKTSQIDTR SARFWASTYG EMMLRVSRNI MLDLESEISC KITLPQIVAK FGTTATMDLG RIHGVKQGDK LSL WHTGAF IDQQGLPRNK VTQSEITLTV SRVYEHEAEL TVDQPELAYS IQIGDVMHKQ M

UniProtKB: Flagellar protein FlgT

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Macromolecule #4: Sodium-type flagellar protein MotY

MacromoleculeName: Sodium-type flagellar protein MotY / type: protein_or_peptide / ID: 4 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 33.587746 KDa
SequenceString: MNKWVITSLF AISTLSASVA SALEVRYMAT PQQSTWQMAT NTPLECRLVH PIPNYGDAEF SSRAGKKINL DFELKMRRPM GDTRNVSLV SMPPVWRPGE GADRITNLQF FKQFDGYIGG QTAWSLLSEL EKGRYPTFSY QDWQSRDQRI EVALSSVLFQ Q PYNEFSDC ...String:
MNKWVITSLF AISTLSASVA SALEVRYMAT PQQSTWQMAT NTPLECRLVH PIPNYGDAEF SSRAGKKINL DFELKMRRPM GDTRNVSLV SMPPVWRPGE GADRITNLQF FKQFDGYIGG QTAWSLLSEL EKGRYPTFSY QDWQSRDQRI EVALSSVLFQ Q PYNEFSDC ISKLLPYSFE DISFTILHYD QGTSVELNKA SQKRLAQIAE YVRYNQDIDL VLVSTYTDST DTNNNSQNLS EQ RAEVLRE YFKSIGLPED RIQVQGYGKR RPIADNASPI GKDKNRRVVI SLGRTQV

UniProtKB: Sodium-type flagellar protein MotY

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Macromolecule #5: Sodium-type flagellar protein MotX

MacromoleculeName: Sodium-type flagellar protein MotX / type: protein_or_peptide / ID: 5 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 24.278615 KDa
SequenceString: MKLRTVAASL LLAWHSSYNP AYAADLGEPV PIYSEAELIK LIEENKHLER VKADNCQIVE DIVARATRIS LPSYEFLYGD MLAWGVCVD QDVELGLYYM ENAAHQGLPA ALEQLGRYYS RGTLVQQDKE RAIPYLREAA AMGNLNARIQ LAELLLRDYG S PLDYEDAY ...String:
MKLRTVAASL LLAWHSSYNP AYAADLGEPV PIYSEAELIK LIEENKHLER VKADNCQIVE DIVARATRIS LPSYEFLYGD MLAWGVCVD QDVELGLYYM ENAAHQGLPA ALEQLGRYYS RGTLVQQDKE RAIPYLREAA AMGNLNARIQ LAELLLRDYG S PLDYEDAY RWLYNSVTAD QRTHNRIALL RQGLERRMPE NIIARAKRRE TFW

UniProtKB: Sodium-type flagellar protein MotX

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Macromolecule #6: Lipoprotein

MacromoleculeName: Lipoprotein / type: protein_or_peptide / ID: 6 / Number of copies: 52 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 16.459971 KDa
SequenceString:
MMKSSLLLLV AALMMTGCQP LQSMRPDDWL TAVGYANISE QRGRDEAEKQ VRAMRASKID AYRELAEQVY GMRISGRAEL QDQRLGTEL TAGAVDGVIR GAEVVRSYKV GDSYVTELRL DIRKMDKMRD YGEVQQVPEK RQMTLF

UniProtKB: Lipoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 25553
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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