[English] 日本語
Yorodumi
- EMDB-39790: Cryo-EM structure of the polar flagellar motor-hook complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39790
TitleCryo-EM structure of the polar flagellar motor-hook complex
Map dataMain map
Sample
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: x 21 types
KeywordsPolar flagellum / Polar flagellar motor / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion ...bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum hook / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting / cell outer membrane / structural molecule activity / plasma membrane / cytosol
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 / : / Flagellar biosynthetic protein FlhB / FlgT, N-terminal domain superfamily / Flagellar basal-body rod FlgF / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod protein FlgB / Flagellar transport protein FliP / Flagellar biosynthesis protein FliR / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar assembly lipoprotein FlgP / Flagellar hook-basal body complex protein FliE / Flagellar hook protein FlgE / Flagellar biosynthetic protein FliQ / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FlhB / Flagellar biosynthetic protein FliR ...Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar assembly lipoprotein FlgP / Flagellar hook-basal body complex protein FliE / Flagellar hook protein FlgE / Flagellar biosynthetic protein FliQ / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FlhB / Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliP / Flagella basal-body protein / Component of sodium-driven polar flagellar motor / Flagellar M-ring protein / Sodium-type flagellar motor component
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 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 polar flagellar motor-hook complex
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

-
Structure visualization

Supplemental images

emd_39790.png

Downloads & links

-
Map

FileDownload / File: emd_39790.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: 0.05
Minimum - Maximum-1.0067507 - 1.1463459
Average (Standard dev.)0.0015328992 (±0.03646179)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: Half map A

Fileemd_39790_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_39790_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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: LRR
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar basal-body rod protein FlgG
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar M-ring protein
    • Protein or peptide: Flagellar basal body rod protein FlgB
    • Protein or peptide: Flagellar basal-body rod protein FlgC
    • Protein or peptide: Flagellar basal-body rod protein FlgF
    • Protein or peptide: Flagellar hook-basal body complex protein FliE
    • Protein or peptide: Flagellar biosynthetic protein FlhB
    • Protein or peptide: Flagella basal-body protein
    • Protein or peptide: FlgH
    • Protein or peptide: Flagellar assembly lipoprotein FlgP
    • Protein or peptide: FlgH
    • Protein or peptide: FlgI
    • Protein or peptide: Component of sodium-driven polar flagellar motor
    • Protein or peptide: Sodium-type flagellar motor component
    • Protein or peptide: FlgB-Dc
    • Protein or peptide: FliE-helix 1

+
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

+
Macromolecule #1: LRR

MacromoleculeName: LRR / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 21.518053 KDa
SequenceString: MRFVSLFLTL MLLCFPSFAY ELDYYSKFGH TDNYGNLDLR NKPYTQLPSG FVVKGNLNIS QTPIKKLPKG LDVGGSLEAT NSALKTIRS GTKIKGYANL LGSKIESWPR GIKLGGYLNL TDTPLKTLPA KLRVKGDLSV IRTPISALPE GLVVDGNLYI G GSALQVFP ...String:
MRFVSLFLTL MLLCFPSFAY ELDYYSKFGH TDNYGNLDLR NKPYTQLPSG FVVKGNLNIS QTPIKKLPKG LDVGGSLEAT NSALKTIRS GTKIKGYANL LGSKIESWPR GIKLGGYLNL TDTPLKTLPA KLRVKGDLSV IRTPISALPE GLVVDGNLYI G GSALQVFP DTMTVKGNIF LGGNKITKWP SNLTLGGAVA P

+
Macromolecule #2: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 31.314904 KDa
SequenceString: MTKGNPIRLL LSTLLLFVGV LFSSFSFAEA EESALPDNLA DGSSVTVQAM QSDTGASRAM SVSSGGGIPA FTMTTNPDGS EDYSVTLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFVMSPV LNEINDKAVQ P YLNEQVTA ...String:
MTKGNPIRLL LSTLLLFVGV LFSSFSFAEA EESALPDNLA DGSSVTVQAM QSDTGASRAM SVSSGGGIPA FTMTTNPDGS EDYSVTLQI LALMTMLGFL PAMVILMTSF TRIVVVMSIL RQAMGLQQTP SNQVIIGIAL FLTFFVMSPV LNEINDKAVQ P YLNEQVTA REAFDAAQAP MKAFMLKQTR IKDLETFVTM SGEQVDNPED VSMAVLIPAF ITSELKTAFQ IGFMLFLPFL II DLVVASV LMAMGMMMLS PMIVSLPFKL MLFVLVDGWN LILSTLAGSF AL

UniProtKB: Flagellar biosynthetic protein FliP

+
Macromolecule #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 10.329615 KDa
SequenceString:
MTPEMFVELF REALWMVLIM VCAIIIPSLL IGLIVAIFQA ATSINEQTLS FLPRLIVTLL ALMLFGHWMT QMLMEYFYGL IERLPQVLY

UniProtKB: Flagellar biosynthetic protein FliQ

+
Macromolecule #4: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 28.905535 KDa
SequenceString: MEYPTSVVLD WIANYFWPYV RISSMLMVMT VTGARFVSPR IRLYLGLAIT FAVMPAIPAV PQDIELLSFR GFMTIAEQMI IGIAMGMVT QFMIQTFVLL GQILGMQSSL GFASMVDPAN GQNTPLLGQL FMFLTTMFFL ATDGHLKMLQ LVVFSFKTLP I GSGSLNAV ...String:
MEYPTSVVLD WIANYFWPYV RISSMLMVMT VTGARFVSPR IRLYLGLAIT FAVMPAIPAV PQDIELLSFR GFMTIAEQMI IGIAMGMVT QFMIQTFVLL GQILGMQSSL GFASMVDPAN GQNTPLLGQL FMFLTTMFFL ATDGHLKMLQ LVVFSFKTLP I GSGSLNAV DFREMAGWLG IMFQTALSMS LSGIIALLTI NLSFGVMTRA APQLNIFSLG FAFALMVGLL LCWYILAGLY SH YEMFWTV GEAQICRLIR LEC

UniProtKB: Flagellar biosynthetic protein FliR

+
Macromolecule #5: Flagellar basal-body rod protein FlgG

MacromoleculeName: Flagellar basal-body rod protein FlgG / type: protein_or_peptide / ID: 5 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 27.908943 KDa
SequenceString: MHPALWVSKT GLDAQQTNIA TISNNLANAS TVGYKKSRAV FEDLFYQNIN QPGGQSSQNT ELPSGLMLGA GSKVVATQKV HTHGNAQTT TNALDMMVEG DGFFQVTLPD GNIGYTRNGQ FTLNGEGTLV TSGSGYPVEP EIVIPEDAIS ITVGTDGEVS V RVRGQQDN ...String:
MHPALWVSKT GLDAQQTNIA TISNNLANAS TVGYKKSRAV FEDLFYQNIN QPGGQSSQNT ELPSGLMLGA GSKVVATQKV HTHGNAQTT TNALDMMVEG DGFFQVTLPD GNIGYTRNGQ FTLNGEGTLV TSGSGYPVEP EIVIPEDAIS ITVGTDGEVS V RVRGQQDN QVVGQLTITD FVNPGGLEPI GQNLYLPTGA SGDPQEGVPG LDGLGEIRQS MLEASNVNVT EELVNMIEAQ RV YEMNSKV ISSVDKMMSF VNQQL

UniProtKB: Flagellar basal-body rod protein FlgG

+
Macromolecule #6: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 6 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 47.434438 KDa
SequenceString: MSYVSLSGLS AAQLDLNTTS NNIANANTYG FKESRAEFAD VYSNSLFTNA KTTPGGGAQA SQVAQQFHEG SSIYTNNPMD LRVSGTGFF AVAKERLTPQ QNELTRNGAF HLNKENYMVT ANDEFLLGYQ VDPSSGEVSS YEPQPINIPA EFGKPKQTAN I EVGVNLPA ...String:
MSYVSLSGLS AAQLDLNTTS NNIANANTYG FKESRAEFAD VYSNSLFTNA KTTPGGGAQA SQVAQQFHEG SSIYTNNPMD LRVSGTGFF AVAKERLTPQ QNELTRNGAF HLNKENYMVT ANDEFLLGYQ VDPSSGEVSS YEPQPINIPA EFGKPKQTAN I EVGVNLPA NGDLKDPTQF DFSDPDTYNR STSSTIYDSM GQSYKLTTYY LKDQTQPNTW NTYYTVTDKE GEKPLNVAAG DA QTPTGHV GHTMKFNNDG TLASLNNGQP ITSVALGDPA TNTTPVDMNG ADPAQTLNFG LGSATQFAAP FELTKFDEDG ATT GFLTKV DFDENGSVMG TYSNGENVTL GRVALVRVPN EQGLDKKGGT QWDSTQFSGD KIWGESNKGS FGTINNGMLE QSNI DMTQE LVDLISAQRN FQANSRSLEV HNQLQQNILQ IR

UniProtKB: Flagellar hook protein FlgE

+
Macromolecule #7: Flagellar M-ring protein

MacromoleculeName: Flagellar M-ring protein / type: protein_or_peptide / ID: 7 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 63.915605 KDa
SequenceString: MADKSTDLTV TEGGSDGALV ASSDVDVESQ NPDLEERSAS KFDMAVGDLD LLRQVVLVLS ISICVALIVM LFFWVKEPEM RPLGAYETE ELIPVLDYLD QQKINYKLDG NTISVESSEY NSIKLGMVRS GVNQATEAGD DILLQDMGFG VSQRLEQERL K LSRERQLA ...String:
MADKSTDLTV TEGGSDGALV ASSDVDVESQ NPDLEERSAS KFDMAVGDLD LLRQVVLVLS ISICVALIVM LFFWVKEPEM RPLGAYETE ELIPVLDYLD QQKINYKLDG NTISVESSEY NSIKLGMVRS GVNQATEAGD DILLQDMGFG VSQRLEQERL K LSRERQLA QAIEEMKQVR KARVLLALPK HSVFVRHNQE ASASVFLTLS TGTNLKQQEV DSIVDMVASA VPGMKTSRIT VT DQHGRLL SSGSQDPASA ARRKEQELER SQEQALREKI DSVLLPILGY GNYTAQVDIQ MDFSAVEQTR KRFDPNTPAT RSE YALEDY NNGNMVAGIP GALSNQPPAD ASIPQDVAQM KDGSVMGQGS VRKESTRNFE LDTTISHERK QTGTVARQTV SVAI KDRRQ VNPDTGEVTY TPMSESEINA IRQVLIGTVG FDQGRGDLLN VLSVKFAEPE AEQLEEPPIW EHPNFSDWVR WFASA LVII VVVLVLVRPA MKKLLNPTSD DEDEMYGPDG LPIGADGETS LIGSDIESSE LFEFGSSIDL PNLHKDEDVL KAVRAL VAN EPELAAQVVK NWMNDNG

UniProtKB: Flagellar M-ring protein

+
Macromolecule #8: Flagellar basal body rod protein FlgB

MacromoleculeName: Flagellar basal body rod protein FlgB / type: protein_or_peptide / ID: 8 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 14.23995 KDa
SequenceString:
MAISFDNALG IHQHTVGVRE RNAEVISTNI AQANTPGYKA RGLDFAKELQ AATSGASIGL SRTDGRHIPA TTTLVGDKLY RLPTQPDTG DGNTVDLDLE RNLFMQNQIR HQASLDFLGS KFKNLTKAIK GE

UniProtKB: Flagellar basal body rod protein FlgB

+
Macromolecule #9: Flagellar basal-body rod protein FlgC

MacromoleculeName: Flagellar basal-body rod protein FlgC / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 14.812569 KDa
SequenceString:
MSLFNVFNVT GSAMSAESVR LNTTSSNLAN ADSVSSSAKD TYKARHAVFG AELSNAMRGG DTVPVKVMGI VESDKPLSAE YNPDHPLAN EEGYIYKPNV NVMEEMANMI SASRAYQTNV QVADSSKQML LRTLQMGQ

UniProtKB: Flagellar basal-body rod protein FlgC

+
Macromolecule #10: Flagellar basal-body rod protein FlgF

MacromoleculeName: Flagellar basal-body rod protein FlgF / type: protein_or_peptide / ID: 10 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 26.987387 KDa
SequenceString: MDRALFLAMS GAKQNMQALQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG HPSRVFSMTE RPGHNFAQGS VITTGRDLDV TIEGSGWIS VLDHTGKEGL TRNGNLKVDQ NGMLTNASGH LVLGENDAPI TLPIPLSKIE IGRDGTISVL PQGAPAEEFQ A VDRIKLVK ...String:
MDRALFLAMS GAKQNMQALQ LRANNLANVS TTGFRADLAQ ARSMQAYGEG HPSRVFSMTE RPGHNFAQGS VITTGRDLDV TIEGSGWIS VLDHTGKEGL TRNGNLKVDQ NGMLTNASGH LVLGENDAPI TLPIPLSKIE IGRDGTISVL PQGAPAEEFQ A VDRIKLVK PNDQSLFKDT NGLFRHKTPN QPYEADATVS LQTGAIEGSN VNAVGEMTAL IDLQRQFEMQ VKMMSTAEEM DK SSDSLLR MS

UniProtKB: Flagellar basal-body rod protein FlgF

+
Macromolecule #11: Flagellar hook-basal body complex protein FliE

MacromoleculeName: Flagellar hook-basal body complex protein FliE / type: protein_or_peptide / ID: 11 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 11.135679 KDa
SequenceString:
MKVDGIQAEM RAMMVEATNT APTASGAKVG ADFNDLLTKA INNVNTLQKA SGDLQTRFDR GDADVSLSDV MIARNKSSVA FDATVQIRN KLVEAYKDLM NMPV

UniProtKB: Flagellar hook-basal body complex protein FliE

+
Macromolecule #12: Flagellar biosynthetic protein FlhB

MacromoleculeName: Flagellar biosynthetic protein FlhB / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 42.197297 KDa
SequenceString: MAESDGQERT EEATPRRLQQ AREKGQVARS KELASASVLI VGAISLMWFG EALARSLFSI MSRLFDLQRE EIFDTAKLFD IALGAMTDL LFPLFLVLAT LFTAAMIGAA GVGGISFSAQ AAMPKLSKMN PLSGLKRMVG MQSWVELIKS ILKVVLVTGV A IYLIQASQ ...String:
MAESDGQERT EEATPRRLQQ AREKGQVARS KELASASVLI VGAISLMWFG EALARSLFSI MSRLFDLQRE EIFDTAKLFD IALGAMTDL LFPLFLVLAT LFTAAMIGAA GVGGISFSAQ AAMPKLSKMN PLSGLKRMVG MQSWVELIKS ILKVVLVTGV A IYLIQASQ ADLIQLSMDV YPQNIFHALD ILLNFILLIS CSLLIVVAID IPFQIWQHAD QLKMTKQEVK DEYKETEGKP EV KGRIRML QREAAQRRMM ADVPQADVIV TNPEHFSVAL RYKQKTDRAP VVIAKGTDHM AMKIREVARE HDITIVPAPP LAR ALYHTT ELEQEIPDGL FTAVAQVLAF VFQLKQYRKR GGQRPKIQDY DLPIPPEHRH

UniProtKB: Flagellar biosynthetic protein FlhB

+
Macromolecule #13: Flagella basal-body protein

MacromoleculeName: Flagella basal-body protein / type: protein_or_peptide / ID: 13 / 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

+
Macromolecule #14: FlgH

MacromoleculeName: FlgH / type: protein_or_peptide / ID: 14 / 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

+
Macromolecule #15: Flagellar assembly lipoprotein FlgP

MacromoleculeName: Flagellar assembly lipoprotein FlgP / type: protein_or_peptide / ID: 15 / 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

+
Macromolecule #16: FlgH

MacromoleculeName: FlgH / type: protein_or_peptide / ID: 16 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 1.45063 KDa
SequenceString:
CAMLEPIETD EVT

+
Macromolecule #17: FlgI

MacromoleculeName: FlgI / type: protein_or_peptide / ID: 17 / 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

+
Macromolecule #18: Component of sodium-driven polar flagellar motor

MacromoleculeName: Component of sodium-driven polar flagellar motor / type: protein_or_peptide / ID: 18 / 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

+
Macromolecule #19: Sodium-type flagellar motor component

MacromoleculeName: Sodium-type flagellar motor component / type: protein_or_peptide / ID: 19 / 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

+
Macromolecule #20: FlgB-Dc

MacromoleculeName: FlgB-Dc / type: protein_or_peptide / ID: 20 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 1.395589 KDa
SequenceString:
IGLSRTDGRH IPA

+
Macromolecule #21: FliE-helix 1

MacromoleculeName: FliE-helix 1 / type: protein_or_peptide / ID: 21 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 1.867152 KDa
SequenceString:
VDGIQAEMRA MMVEATN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 329955
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C100 (100 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelModelAngelo
RefinementProtocol: OTHER
Output model

PDB-8z60:
Cryo-EM structure of the polar flagellar motor-hook complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more