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- EMDB-72848: T-ring-PomB complex in Vibrio cholerae -

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Basic information

Entry
Database: EMDB / ID: EMD-72848
TitleT-ring-PomB complex in Vibrio cholerae
Map dataT-ring-PomB complex in Vibrio cholerae.
Sample
  • Cell: Vibrio cholerae
    • Protein or peptide: Sodium-type flagellar protein MotX
    • Protein or peptide: Sodium-type flagellar protein MotY
    • Protein or peptide: Chemotaxis protein PomB
KeywordsIn situ cryo-EM / sheathed flagellar motor / Vibrio cholerae / T-ring / PomB / assembled state / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent cell motility / cell outer membrane
Similarity search - Function
MotY N-terminal domain / MotY N-terminal domain / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. ...MotY N-terminal domain / MotY N-terminal domain / : / Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Sodium-type flagellar protein MotX / Sodium-type flagellar protein MotY / Chemotaxis protein PomB
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.98 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_72848.png

Downloads & links

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Map

FileDownload / File: emd_72848.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT-ring-PomB complex in Vibrio cholerae.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.028117515 - 1.6696577
Average (Standard dev.)0.0006705874 (±0.015132774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72848_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: T-ring-PomB complex in Vibrio cholerae.

Fileemd_72848_additional_1.map
AnnotationT-ring-PomB complex in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T-ring-PomB complex in Vibrio cholerae.

Fileemd_72848_half_map_1.map
AnnotationT-ring-PomB complex in Vibrio cholerae.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T-ring-PomB complex in Vibrio cholerae.

Fileemd_72848_half_map_2.map
AnnotationT-ring-PomB complex in Vibrio cholerae.
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

EntireName: Vibrio cholerae (bacteria)
Components
  • Cell: Vibrio cholerae
    • Protein or peptide: Sodium-type flagellar protein MotX
    • Protein or peptide: Sodium-type flagellar protein MotY
    • Protein or peptide: Chemotaxis protein PomB

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Supramolecule #1: Vibrio cholerae

SupramoleculeName: Vibrio cholerae / 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: Sodium-type flagellar protein MotX

MacromoleculeName: Sodium-type flagellar protein MotX / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Sodium-type flagellar protein MotY

MacromoleculeName: Sodium-type flagellar protein MotY / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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 #3: Chemotaxis protein PomB

MacromoleculeName: Chemotaxis protein PomB / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Molecular weightTheoretical: 17.542775 KDa
SequenceString:
QQQAQAMSEQ METVAESIKK ALSREIEQGA IEVENLGQQI DIRIREKGAF PEGSAFLQPK FRPLVRQIAE LVKDIPGKVR VTGHTDNQK LDSELYRSNW DLSAQRAVSV AQEMEKVKDF DHLRLQVRGL ADTQPLGPND TEAQRATNRR VEISIL

UniProtKB: Chemotaxis protein PomB

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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

MicroscopeFEI TECNAI F30
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 opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 697164
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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