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- EMDB-72947: LPHT-ring subunit with C13 MotX in Vibrio cholerae at assembled state -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72947
TitleLPHT-ring subunit with C13 MotX in Vibrio cholerae at assembled state
Map data
Sample
  • Organelle or cellular component: 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: Flagellar assembly lipoprotein FlgP
KeywordsIn situ cryo-EM / Vibrio cholerae / T-ring / 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
Flagellar assembly lipoprotein FlgP / Sodium-type flagellar protein MotX / Flagellar protein FlgT / 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: 3.6 Å
AuthorsGuo W / Yue J / Liu J
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI189907 United States
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI189907 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI102584 United States
CitationJournal: To Be Published
Title: T-ring subunit in Vibrio cholerae at assembled state.
Authors: Wangbiao G / Jian Y / Jun L
History
DepositionSep 29, 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_72947.png

Downloads & links

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Map

FileDownload / File: emd_72947.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 318 pix.
= 477.636 Å		1.5 Å/pix.
x 318 pix.
= 477.636 Å		1.5 Å/pix.
x 318 pix.
= 477.636 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.502 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.3890636 - 0.811417
Average (Standard dev.)0.009721358 (±0.05872635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 477.636 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72947_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_72947_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72947_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_72947_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 : Vibrio cholerae DflhG

EntireName: Vibrio cholerae DflhG
Components
  • Organelle or cellular component: 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: Flagellar assembly lipoprotein FlgP

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Supramolecule #1: Vibrio cholerae DflhG

SupramoleculeName: Vibrio cholerae DflhG / type: organelle_or_cellular_component / 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: 24.25652 KDa
SequenceString: TTTVDAVEGD KSESNSGLTD ALRNRTDPVA GDPAWAPIHP KGKPEHYAAE TGSLFNLASS SSMYDDSKPR GVGDIITVTL NESTKAAKS ADADLNKKND ASMDPLAVGG KDLTIGDYNF SYALKNDNKF SGSAAANQSN SMSGSITVEV IEVLANGNLV I RGEKWLTL ...String:
TTTVDAVEGD KSESNSGLTD ALRNRTDPVA GDPAWAPIHP KGKPEHYAAE TGSLFNLASS SSMYDDSKPR GVGDIITVTL NESTKAAKS ADADLNKKND ASMDPLAVGG KDLTIGDYNF SYALKNDNKF SGSAAANQSN SMSGSITVEV IEVLANGNLV I RGEKWLTL NTGDEYIRLS GTIRPDDIDF DNTIASNRIS NARIQYSGTG TNQDMQEPGF LARFFNVSL

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: 35.702562 KDa
SequenceString: ARIKDVAQVA GVRNNQLVGY GLVTGLPGTG ESTPFTDQSF NAMLQSFGIQ LPPGTKPKTK NVAAVIVTAD LPAFSKQGQT IDITVSSIG SAKSLRGGTL MQTFLKGLDG QVYAVAQGNL VVSGFSATGA DGSKIVGNNP TVGMISSGAI VEREVPNPFG R GDYITFNL ...String:
ARIKDVAQVA GVRNNQLVGY GLVTGLPGTG ESTPFTDQSF NAMLQSFGIQ LPPGTKPKTK NVAAVIVTAD LPAFSKQGQT IDITVSSIG SAKSLRGGTL MQTFLKGLDG QVYAVAQGNL VVSGFSATGA DGSKIVGNNP TVGMISSGAI VEREVPNPFG R GDYITFNL FESDFTTAQR LADAVNQFLG PQMASAVDAA SIKVRAPRDL SQRVAFLSAI ENLEFNPADS AAKIIVNSRT GT IVVGQNV RLKPAAVTHG GMTVAIKENL NVSQPNALGG GQTVVVPNTE IEVTEKQGKM FKLEPGVTLD DLVRAVNEVG AAP SDLMAI LQALKQAGAI EGQLIII

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: 39.808223 KDa
SequenceString: YEVTGSAAIV SSEEVARLHA LEDALYKAVN FAGADIGSIS NLMPLLESDR REYLFANHEV RYILIEERKA INNVMYVRTR IDIYPSATA CHVEQYKKTM LIGNIDLASP QQAVMGQIYQ VGDDFAQVIN RRLEQESRSF VSVGTTQYDI DPKAPERIKM I AQDAGAQY ...String:
YEVTGSAAIV SSEEVARLHA LEDALYKAVN FAGADIGSIS NLMPLLESDR REYLFANHEV RYILIEERKA INNVMYVRTR IDIYPSATA CHVEQYKKTM LIGNIDLASP QQAVMGQIYQ VGDDFAQVIN RRLEQESRSF VSVGTTQYDI DPKAPERIKM I AQDAGAQY IMGGMITDLT ATIEQKTLQD DIINRQFAME ISVFDGKTGN EVMTRTYREV ARWPFPKTSQ IDTRSARFWA ST YGEMMLR VSRNIMLDLE SEISCKITLP QIVAKFGTTA TMDLGRIHGV KQGDKLSLWH TGAFIDQQGL PRNKVTQSEI TLT VSRVYE HEAELTVDQP ELAYSIQIGD VMHKQM

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: 31.307084 KDa
SequenceString: LEVRYMATPQ QSTWQMATNT PLECRLVHPI PNYGDAEFSS RAGKKINLDF ELKMRRPMGD TRNVSLVSMP PVWRPGEGAD RITNLQFFK QFDGYIGGQT AWSLLSELEK GRYPTFSYQD WQSRDQRIEV ALSSVLFQQP YNEFSDCISK LLPYSFEDIS F TILHYDQG ...String:
LEVRYMATPQ QSTWQMATNT PLECRLVHPI PNYGDAEFSS RAGKKINLDF ELKMRRPMGD TRNVSLVSMP PVWRPGEGAD RITNLQFFK QFDGYIGGQT AWSLLSELEK GRYPTFSYQD WQSRDQRIEV ALSSVLFQQP YNEFSDCISK LLPYSFEDIS F TILHYDQG TSVELNKASQ KRLAQIAEYV RYNQDIDLVL VSTYTDSTDT NNNSQNLSEQ RAEVLREYFK SIGLPEDRIQ VQ GYGKRRP IADNASPIGK DKNRRVVISL GRTQV

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: 21.729629 KDa
SequenceString:
ADLGEPVPIY SEAELIKLIE ENKHLERVKA DNCQIVEDIV ARATRISLPS YEFLYGDMLA WGVCVDQDVE LGLYYMENAA HQGLPAALE QLGRYYSRGT LVQQDKERAI PYLREAAAMG NLNARIQLAE LLLRDYGSPL DYEDAYRWLY NSVTADQRTH N RIALLRQG LERRMPENII ARAKRRETFW

UniProtKB: Sodium-type flagellar protein MotX

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Macromolecule #6: Flagellar assembly lipoprotein FlgP

MacromoleculeName: Flagellar assembly lipoprotein FlgP / 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: 1.792062 KDa
SequenceString:
GEVQQVPEKR QMTLF

UniProtKB: Flagellar assembly lipoprotein FlgP

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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: 2.7 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53628
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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