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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 / Sel1 repeat / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / 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 / : / : / 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: Protein Cell / Year: 2026
Title: Molecular basis of high-torque transmission of the Vibrio polar flagellar motor.
Authors: Ling Zhang / Jiaxing Tan / Xuemin Duan / Xiaofei Wang / Ting Wang / Keke Yuan / Michio Homma / Seiji Kojima / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission ...The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission of varying torques to flagellar filaments to grant bacteria diverse swimming capabilities. Compared to peritrichous flagellar motors, polar flagellar motors are faster machines that transmit higher torque to drive high-speed motility in liquids and empower swimming in viscous environments. However, structural basis of high-torque transmission of the polar flagellar motors is still unclear. Here we present a cryo-electron microscopy structure of the polar flagellar motor in complex with the hook from Vibrio alginolyticus, comprising 295 subunits from 18 proteins. Compared to the peritrichous flagellar rod, this structure reveals an increased number of inter-subunit interactions in the rod of the polar flagellar motor. Nine phospholipid molecules insert into the interface between the export apparatus and the proximal rod. The LP ring contains more electrostatic charges on the inner surface and has fewer physical contacts with the rod, while the HT ring tightly binds to the outer surface of the LP ring. FlrP, a protein of previously unknown function, is identified as a new component of the polar flagellar motor, and extensively participates in the interactions of 15 FliF peptides of the MS ring with the rod. In contrast to that in the peritrichous flagellum, the hook in the polar flagellum has two different conformational states, L- and R-types. These findings provide unprecedented insights into structural adaptations of the bacterial polar flagellar motors for high-torque transmission.
History
DepositionApr 18, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing 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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