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- EMDB-39776: Cryo-EM structure of the LPHT ring -

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Basic information

Entry
Database: EMDB / ID: EMD-39776
TitleCryo-EM structure of the LPHT ring
Map dataMain map
Sample
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: Component of sodium-driven polar flagellar motor
    • Protein or peptide: Sodium-type flagellar motor component
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar assembly lipoprotein FlgP
    • Protein or peptide: The N-terminus of Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagella basal-body protein
KeywordsPolar flagellum / Polar flagellar motor / LPHT ring / Bushing / MOTOR PROTEIN
Function / homology
Function and homology information


cell outer membrane
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 / MotY N-terminal domain / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP ...Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / MotY N-terminal domain / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP / : / FlgT, N-terminal domain superfamily / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Flagellar assembly lipoprotein FlgP / : / : / Flagella basal-body protein / Component of sodium-driven polar flagellar motor / Sodium-type flagellar motor component
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsZhang L / Tan JX / 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 LPHT ring
Authors: Zhang L / Tan JX / Zhou Y / Zhu YQ
History
DepositionApr 18, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39776.png

Downloads & links

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Map

FileDownload / File: emd_39776.map.gz / Format: CCP4 / Size: 909.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 620 pix.
= 744. Å		1.2 Å/pix.
x 620 pix.
= 744. Å		1.2 Å/pix.
x 620 pix.
= 744. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-2.6612427 - 3.8611612
Average (Standard dev.)0.00019218415 (±0.119865805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions620620620
Spacing620620620
CellA=B=C: 744.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_39776_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_39776_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The polar flagellar motor-hook complex

EntireName: The polar flagellar motor-hook complex
Components
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: Component of sodium-driven polar flagellar motor
    • Protein or peptide: Sodium-type flagellar motor component
    • Protein or peptide: Flagellar L-ring protein
    • Protein or peptide: Flagellar assembly lipoprotein FlgP
    • Protein or peptide: The N-terminus of Flagellar L-ring protein
    • Protein or peptide: Flagellar P-ring protein
    • Protein or peptide: Flagella basal-body protein

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Supramolecule #1: The polar flagellar motor-hook complex

SupramoleculeName: The polar flagellar motor-hook complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148

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Macromolecule #1: Component of sodium-driven polar flagellar motor

MacromoleculeName: Component of sodium-driven polar flagellar motor / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 33.528008 KDa
SequenceString: MKKWLITSGV VFSLFSTSSF AVMGKRYVAT PQQSQWEMVV NTPLECQLVH PIPSFGDAVF SSRANKKINL DFELKMRRPM GETRNVSLI SMPPPWRPGE HADRITNLKF FKQFDGYVGG QTAWGILSEL EKGRYPTFSY QDWQSRDQRI EVALSSVLFQ N KYNAFSDC ...String:
MKKWLITSGV VFSLFSTSSF AVMGKRYVAT PQQSQWEMVV NTPLECQLVH PIPSFGDAVF SSRANKKINL DFELKMRRPM GETRNVSLI SMPPPWRPGE HADRITNLKF FKQFDGYVGG QTAWGILSEL EKGRYPTFSY QDWQSRDQRI EVALSSVLFQ N KYNAFSDC ISNLLKYSFE DIAFTILHYE RQGDQLTKAS KKRLSQIADY IRHNQDIDLV LVATYTDSTD GKSASQSLSE RR AESLRDY FQSLGLPEDR IQVQGYGKRR PIADNGSPIG KDKNRRVVIS LGRTQV

UniProtKB: Component of sodium-driven polar flagellar motor

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Macromolecule #2: Sodium-type flagellar motor component

MacromoleculeName: Sodium-type flagellar motor component / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 24.088613 KDa
SequenceString: MKLRTVAASL LLTLVATTAK ANVADVGAPV PIYTEAELIK LIEQNKHLQR VRADNCQLVE DIVARATRIN LPAYEFLYGD MLAWGVCVE QDVELGLYYI ENAAHQGLPA ALEQIGRYYS RGTLVQQDKE RAIPYLREAA SMGNLNARIH LAELLLRDYG S PLDYEDAY ...String:
MKLRTVAASL LLTLVATTAK ANVADVGAPV PIYTEAELIK LIEQNKHLQR VRADNCQLVE DIVARATRIN LPAYEFLYGD MLAWGVCVE QDVELGLYYI ENAAHQGLPA ALEQIGRYYS RGTLVQQDKE RAIPYLREAA SMGNLNARIH LAELLLRDYG S PLDYEDAY RWLYNSVTAD KRQHKRITVL RNGLEQRMPQ NVIARAKRRD TFW

UniProtKB: Sodium-type flagellar motor component

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Macromolecule #3: Flagellar L-ring protein

MacromoleculeName: Flagellar L-ring protein / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 27.929951 KDa
SequenceString: MKRICLLALI ATMSGCAMLE PIETDEVTQA TTVVDAVEGD KSKEESSGIV DTLRGRSDPV AGDPAWAPIH PKKKPEHYAA ATGSLFSAE HITDLYDDSK PRGIGDIITV TLDETTSATK SANADLSKTN EAQMDPLQVG GEELQIGGKY NFSYDLNNSN S FAGDSSAK ...String:
MKRICLLALI ATMSGCAMLE PIETDEVTQA TTVVDAVEGD KSKEESSGIV DTLRGRSDPV AGDPAWAPIH PKKKPEHYAA ATGSLFSAE HITDLYDDSK PRGIGDIITV TLDETTSATK SANADLSKTN EAQMDPLQVG GEELQIGGKY NFSYDLNNSN S FAGDSSAK QSNSISGYIT VEVIEVLANG NLVIRGEKWM TLNTGDEYIR LSGTIRPDDI SFDNTIASNR VSNARIQYSG TG VQQDMQE PGFLARFFNV AL

UniProtKB: UNIPROTKB: A0A9W4BB53

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Macromolecule #4: Flagellar assembly lipoprotein FlgP

MacromoleculeName: Flagellar assembly lipoprotein FlgP / type: protein_or_peptide / ID: 4 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 16.30376 KDa
SequenceString:
MKKLLFIVAT LILVGCQPLQ QMRQDEILVA VGYASVSEQT GRTVEEKRVR AMRASKIDAY RELAEQVYGM RVSGRAELQD QRLGIESTT GAVDGVIRGA EVVRSYLVED SYVTELRLDI RKMDKLRDYG EVQQVPEKRQ QTLF

UniProtKB: Flagellar assembly lipoprotein FlgP

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Macromolecule #5: The N-terminus of Flagellar L-ring protein

MacromoleculeName: The N-terminus of Flagellar L-ring protein / type: protein_or_peptide / ID: 5 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 1.45063 KDa
SequenceString:
CAMLEPIETD EVT

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Macromolecule #6: Flagellar P-ring protein

MacromoleculeName: Flagellar P-ring protein / type: protein_or_peptide / ID: 6 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 37.892234 KDa
SequenceString: MKKLLLILMS VALFSTAAQA ARIKDVAQVA GVRSNQLVGY GLVSGLPGTG EANPFTEQSF AAMLQNFGIQ MPPGTKPKIK NVAAVMVTA ELPPFSKPGQ QVDVTVSSIG SAKSLRGGTL LQTFLKGLDG QVYAVAQGNL VVSGFSAEGA DGSKIVGNNP T VGLISSGA ...String:
MKKLLLILMS VALFSTAAQA ARIKDVAQVA GVRSNQLVGY GLVSGLPGTG EANPFTEQSF AAMLQNFGIQ MPPGTKPKIK NVAAVMVTA ELPPFSKPGQ QVDVTVSSIG SAKSLRGGTL LQTFLKGLDG QVYAVAQGNL VVSGFSAEGA DGSKIVGNNP T VGLISSGA TVEREIPNPF GRGDYITFNL LESDFTTAQR MADAVNNFLG PQMASAVDAT SVRVRAPRDV SQRVAFLSAI EN LEFDPAD GAAKIIVNSR TGTIVVGKHV RLKPAAVTHG GMTVAIKENL NVSQPNGFSG GQTVVVPDSD IEVSEEQGKM FKF EPGLTL DDLVRAVNQV GAAPSDLMAI LQALKQAGAI EGQLIII

UniProtKB: UNIPROTKB: A0A9W4BSQ4

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Macromolecule #7: Flagella basal-body protein

MacromoleculeName: Flagella basal-body protein / type: protein_or_peptide / ID: 7 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 42.417168 KDa
SequenceString: MKKILNSLFS ITLVMLVPFK VMASWYEVTG VATIVSSEET ARLHALEDAL FKAVNFSGAD IGSISNLMPL LEESRNEYQF TNHEVRYIL VESERKRRGK VEVKIRVDIY PSATGCHTDQ YKKTILVGNI EVASPQQAVM GQIYQVGDDF SRVVNRQLDQ T SRSFVSVG ...String:
MKKILNSLFS ITLVMLVPFK VMASWYEVTG VATIVSSEET ARLHALEDAL FKAVNFSGAD IGSISNLMPL LEESRNEYQF TNHEVRYIL VESERKRRGK VEVKIRVDIY PSATGCHTDQ YKKTILVGNI EVASPQQAVM GQIYQVGDDF SRVVNRQLDQ T SRSFVSVG TTDYSISSNY PARTQMIAQD NGAQYIIGGV ITDLTATVES QLLQDDIINR QFALEMKVFD GKTGHEVFNK AY REVARWP FAKTSQVDTR SARFWASTYG EMMLRVSRNI MLDLESELSC KITLPEVVAV FGNTVTMDLG RMHGVKEGDK LQL WHTASF IDQNGLPRNK VSQSEITLTV SRIYEHEAEL TIDQPNLASS VQIGDVMNKI L

UniProtKB: Flagella basal-body protein

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 329955
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45233
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8z5n:
Cryo-EM structure of the LPHT ring

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