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- EMDB-51557: Campylobacter hook-filament junction-cap complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51557
TitleCampylobacter hook-filament junction-cap complex
Map dataCampylobacter cap-junction complex
Sample
  • Organelle or cellular component: Hook-filament junction-cap complex in Campylobacter jejuni
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar hook-associated protein 1
    • Protein or peptide: Flagellar hook-associated protein 2
KeywordsCampylobacter jejuni / flagellar cap / hook-filament junction / FliD / FlgK / FlgL / flagella / TRANSPORT PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cell adhesion / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif ...Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif / 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 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellin / Flagellar hook-associated protein 1 / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsQin K / Gonzalez-Rodriguez N / Shmakova E / Beeby M / Bergeron JRC
Funding support United Kingdom, France, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V000799/1 United Kingdom
Human Frontier Science Program (HFSP)RGP0028/2021-HOCHBERG France
CitationJournal: To Be Published
Title: Structure of the complete extracellular bacterial flagellum reveals mechanism for flagellin incorporation
Authors: Qin K / Einenkel R / Al-Otaibi NS / Schmidt J / Mann D / Drobnic T / Cohen EJ / Gonzalez-Rodriguez N / Harrowell J / Shmakova E / Beeby M / Erhardt M / Bergeron JRC
History
DepositionSep 16, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51557.png

Downloads & links

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Map

FileDownload / File: emd_51557.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCampylobacter cap-junction complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 300 pix.
= 660. Å		2.2 Å/pix.
x 300 pix.
= 660. Å		2.2 Å/pix.
x 300 pix.
= 660. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.04949203 - 0.06972969
Average (Standard dev.)-0.000000000000005 (±0.00291173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 660.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_51557_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_51557_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hook-filament junction-cap complex in Campylobacter jejuni

EntireName: Hook-filament junction-cap complex in Campylobacter jejuni
Components
  • Organelle or cellular component: Hook-filament junction-cap complex in Campylobacter jejuni
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar hook-associated protein 1
    • Protein or peptide: Flagellar hook-associated protein 2

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Supramolecule #1: Hook-filament junction-cap complex in Campylobacter jejuni

SupramoleculeName: Hook-filament junction-cap complex in Campylobacter jejuni
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Campylobacter jejuni (Campylobacter)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 82.047 KDa
SequenceString: MRITNKLNFT NSVNNSMGGQ SALYQISQQL ASGLKIQNSY EDASTYIDNT RLEYEIKTLE QVKESTSRAQ EMTQNSMKAL QDMVKLLED FKVKVTQAAS DSNSQTSREA IAKELERIKE SIVQLANTSV NGQYLFAGSQ VANKPFDSNG NYYGDKNNIN V VTGAGTES ...String:
MRITNKLNFT NSVNNSMGGQ SALYQISQQL ASGLKIQNSY EDASTYIDNT RLEYEIKTLE QVKESTSRAQ EMTQNSMKAL QDMVKLLED FKVKVTQAAS DSNSQTSREA IAKELERIKE SIVQLANTSV NGQYLFAGSQ VANKPFDSNG NYYGDKNNIN V VTGAGTES PYNIPGWDLF FKADGDYKKQ ISTNVSFTDN RWDLNKDPDK TKYLTGDSKW QQLIGQGYVK DNSLDADKDF EY DDSKLDF PPTTLYVQGT KPDGTSFKSA VLVKPEDTLE DVMENIGALY GNTPNNKVVE VSMNDSGQIQ ITDLKQGNNK LDF HAVAFT PQADTKDELK NIIEAANQEG ISMNEVTNRV MQASTAAPSN GDITKLNNPV TVTINNQQFT IDLKQTDFIK SKMT DTDGN AANGADYDNV YFEKNGNTVY GNVSQVIKGS NAYATDSTKL SEVMAGDSLN GTTLNLKVNS KGGNSYDVTI NLQTS TVSY PDPNNPGQTI SFPIMHTNPA TGNSGVVTGS NDITYGQIND IIGMFAADKI PTTTIQANNG QINNADYTQI QQLMKD SQA TVDVSMDYKG RISVTDKLSS GTNIEISLSD SQSGQFPAPP FTTTSTVQNG PNFSFSANNS LTIDEPNVDI IKDLDSM ID AVLKGNMRAD SESENPRNTG MQGALERLDH LADHVSKLNT TMGAYHNTIE GVNTRTSFLS VNVQSIKSNV IDVDYGEA M MNLMQVQLAY QASLKASTTI SQLSLLNYM

UniProtKB: Flagellin

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Macromolecule #2: Flagellar hook-associated protein 1

MacromoleculeName: Flagellar hook-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 67.121469 KDa
SequenceString: MGIFGTLYTG VTGLKASEVQ IATTGNNISN ANATFYTRQR VVQTTNGYIT TGGVQVGTGT AVESIVRLHD EYSYYKLKGA SNQLEYTKY MASTLQEIAQ RFPDLQNTGI LQDLENYNKA WNDFASNPNE NATKIALVKA SQTLTESVNN TFATLDKIQK K VNDDIKNT ...String:
MGIFGTLYTG VTGLKASEVQ IATTGNNISN ANATFYTRQR VVQTTNGYIT TGGVQVGTGT AVESIVRLHD EYSYYKLKGA SNQLEYTKY MASTLQEIAQ RFPDLQNTGI LQDLENYNKA WNDFASNPNE NATKIALVKA SQTLTESVNN TFATLDKIQK K VNDDIKNT VDEINKIGEE IATINKQIYG QEALPTEHAN ELRDRRDELE LTLSKLVSAV ASKNEINQDN RLDTTITDPG HQ YNLSIEG FSIVDGINFH PLKLDYDDKN KSYSIYYETP DEKVRDLTAK ISGGQLGAQL DLRGRNYSKS EGKYEDGIIQ GYM DSLDTF AKTMINETNN LYASSAKSSV TSDYLSGLKG DIPLVNYDRT IQPGSFDIVI YDDKGDKKLT KTITIDVNTT MNDI MRQIN ANTDDNDNKN SNDDVDDHIN ASFSYDAKTG DGLFQINAKS GFKVAIEDKG TNFAGAFSIG GFFSGTDASD MKVKD SILN DPSTVRASSN GVDSGNDMAN KIIQLQYDKV NFYNEDGTID NLTMEEYYRK LTGKIASDGE NNNVVNSSNE TLYNSV YSE YQSKSGVNTN EELAALIQYQ SSYGAAAKIV STVDQMLDTL LGLKS

UniProtKB: Flagellar hook-associated protein 1

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Macromolecule #3: Flagellar hook-associated protein 2

MacromoleculeName: Flagellar hook-associated protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 69.843852 KDa
SequenceString: MAFGSLSSLG FGSGVLTQDT IDKLKEAEQK ARIDPYTKKI EENTTKQKDL TEIKTKLLSF QTAVSSLADA TVFAKRKVVG SISDNPPAS LTVNSGVALQ SMNINVTQLA QKDVYQSKGL ANDGGFVNAQ LNGTADLTFF SNGKEYTVTV DKNTTYRDLA D KINEASGG ...String:
MAFGSLSSLG FGSGVLTQDT IDKLKEAEQK ARIDPYTKKI EENTTKQKDL TEIKTKLLSF QTAVSSLADA TVFAKRKVVG SISDNPPAS LTVNSGVALQ SMNINVTQLA QKDVYQSKGL ANDGGFVNAQ LNGTADLTFF SNGKEYTVTV DKNTTYRDLA D KINEASGG EIVAKIVNTG EKGTPYRLTL TSKETGEDSA ISFYAGKKDS NGKYQKDINA EKIFDDLGWG LDVSASIDPD KD KKGYGIK DASLHIQTAQ NAEFTLDGIK MFRSSNTVTD LGVGMTLTLN KTGEINFDVQ QDFEGVTKAM QDLVDAYNDL VTN LNAATD YNSETGTKGT LQGISEVNSI RSSILADLFD SQVVDGTTED ANGNKVNTKV MLSMQDFGLS LNDAGTLSFD SSKF EQKVK EDPDSTESFF SNITKYEDIN HTGEVIKTGS LSKYLNSNGG NTNGLEFKPG DFTIVFNNQT YDLSKNSDGT NFKLT GKTE EELLQNLANH INSKGIEGLK VKVESYNQNN VTGFRLNFSG DGSSDFSIKG DANILKELGL SDVNITSKPI EGKGIF SKL KATLQEMTGK DGSITKYDES LTNDIKSLNT SKDSTQAMID TRYDTMANQW LQYESILNKL NQQLNTVTNM INAANNS NN

UniProtKB: Flagellar hook-associated protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (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: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15077
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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