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- EMDB-44735: Structural basis for adhesin secretion by the outer-membrane ushe... -

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Basic information

Entry
Database: EMDB / ID: EMD-44735
TitleStructural basis for adhesin secretion by the outer-membrane usher in type 1 pili
Map dataDeepEMhancer map
Sample
  • Complex: Quaternary complex of the FimD usher translocating the FimH adhesin with FimC chaperone and FimF tip adapter on the periplasmic side
    • Protein or peptide: Outer membrane usher protein FimD
    • Protein or peptide: Protein FimF
    • Protein or peptide: Type 1 fimbria chaperone FimC
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
KeywordsOuter membrane usher / FimD / FimH / adhesin / type 1 pilus / TRANSPORT PROTEIN
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : ...fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / : / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. ...Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein FimF / Type 1 fimbrin D-mannose specific adhesin / Outer membrane usher protein FimD / Type 1 fimbria chaperone FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsBitter RM / Zimmerman M / Hultgren S / Yuan P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI157797 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural basis for adhesin secretion by the outer-membrane usher in type 1 pili.
Authors: Ryan M Bitter / Maxwell I Zimmerman / Brock T Summers / Jerome S Pinkner / Karen W Dodson / Scott J Hultgren / Peng Yuan /
Abstract: Gram-negative bacteria produce chaperone-usher pathway pili, which are extracellular protein fibers tipped with an adhesive protein that binds to a receptor with stereochemical specificity to ...Gram-negative bacteria produce chaperone-usher pathway pili, which are extracellular protein fibers tipped with an adhesive protein that binds to a receptor with stereochemical specificity to determine host and tissue tropism. The outer-membrane usher protein, together with a periplasmic chaperone, assembles thousands of pilin subunits into a highly ordered pilus fiber. The tip adhesin in complex with its cognate chaperone activates the usher to allow extrusion across the outer membrane. The structural requirements to translocate the adhesin through the usher pore from the periplasm to the extracellular space remains incompletely understood. Here, we present a cryoelectron microscopy structure of a quaternary tip complex in the type 1 pilus system from , which consists of the usher FimD, chaperone FimC, adhesin FimH, and the tip adapter FimF. In this structure, the usher FimD is caught in the act of secreting its cognate adhesin FimH. Comparison with previous structures depicting the adhesin either first entering or having completely exited the usher pore reveals remarkable structural plasticity of the two-domain adhesin during translocation. Moreover, a piliation assay demonstrated that the structural plasticity, enabled by a flexible linker between the two domains, is a prerequisite for adhesin translocation through the usher pore and thus pilus biogenesis. Overall, this study provides molecular details of adhesin translocation across the outer membrane and elucidates a unique conformational state adopted by the adhesin during stepwise secretion through the usher pore. This study elucidates fundamental aspects of FimH and usher dynamics critical in urinary tract infections and is leading to antibiotic-sparing therapeutics.
History
DepositionMay 3, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44735.png

Downloads & links

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Map

FileDownload / File: emd_44735.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 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: 0.311
Minimum - Maximum-0.0016748268 - 2.2028782
Average (Standard dev.)0.0013188769 (±0.02566651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Map

Fileemd_44735_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_44735_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_44735_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 : Quaternary complex of the FimD usher translocating the FimH adhes...

EntireName: Quaternary complex of the FimD usher translocating the FimH adhesin with FimC chaperone and FimF tip adapter on the periplasmic side
Components
  • Complex: Quaternary complex of the FimD usher translocating the FimH adhesin with FimC chaperone and FimF tip adapter on the periplasmic side
    • Protein or peptide: Outer membrane usher protein FimD
    • Protein or peptide: Protein FimF
    • Protein or peptide: Type 1 fimbria chaperone FimC
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin

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Supramolecule #1: Quaternary complex of the FimD usher translocating the FimH adhes...

SupramoleculeName: Quaternary complex of the FimD usher translocating the FimH adhesin with FimC chaperone and FimF tip adapter on the periplasmic side
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Outer membrane usher protein FimD

MacromoleculeName: Outer membrane usher protein FimD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 91.439914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDA CVPLTTMVQD ATAHLDVGQQ RLNLTIPQAF MSNRARGYIP PELWDPGINA GLLNYNFSGN SVQNRIGGNS H YAYLNLQS ...String:
DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDA CVPLTTMVQD ATAHLDVGQQ RLNLTIPQAF MSNRARGYIP PELWDPGINA GLLNYNFSGN SVQNRIGGNS H YAYLNLQS GLNIGAWRLR DNTTWSYNSS DRSSGSKNKW QHINTWLERD IIPLRSRLTL GDGYTQGDIF DGINFRGAQL AS DDNMLPD SQRGFAPVIH GIARGTAQVT IKQNGYDIYN STVPPGPFTI NDIYAAGNSG DLQVTIKEAD GSTQIFTVPY SSV PLLQRE GHTRYSITAG EYRSGNAQQE KPRFFQSTLL HGLPAGWTIY GGTQLADRYR AFNFGIGKNM GALGALSVDM TQAN STLPD DSQHDGQSVR FLYNKSLNES GTNIQLVGYR YSTSGYFNFA DTTYSRMNGY NIETQDGVIQ VKPKFTDYYN LAYNK RGKL QLTVTQQLGR TSTLYLSGSH QTYWGTSNVD EQFQAGLNTA FEDINWTLSY SLTKNAWQKG RDQMLALNVN IPFSHW LRS DSKSQWRHAS ASYSMSHDLN GRMTNLAGVY GTLLEDNNLS YSVQTGYAGG GDGNSGSTGY ATLNYRGGYG NANIGYS HS DDIKQLYYGV SGGVLAHANG VTLGQPLNDT VVLVKAPGAK DAKVENQTGV RTDWRGYAVL PYATEYRENR VALDTNTL A DNVDLDNAVA NVVPTRGAIV RAEFKARVGI KLLMTLTHNN KPLPFGAMVT SESSQSSGIV ADNGQVYLSG MPLAGKVQV KWGEEENAHC VANYQLPPES QQQLLTQLSA ECR

UniProtKB: Outer membrane usher protein FimD

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Macromolecule #2: Protein FimF

MacromoleculeName: Protein FimF / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.177095 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADSTITIRGY VRDNGCSVAA ESTNFTVDLM ENAAKQFNNI GATTPVVPFR ILLSPCGNAV SAVKVGFTGV ADSHNANLLA LENTVSAAS GLGIQLLNEQ QNQIPLNAPS SALSWTTLTP GKPNTLNFYA RLMATQVPVT AGHINATATF TLEYQ

UniProtKB: Protein FimF

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Macromolecule #3: Type 1 fimbria chaperone FimC

MacromoleculeName: Type 1 fimbria chaperone FimC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.552932 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GVALGATRVI YPAGQKQVQL AVTNNDENST YLIQSWVENA DGVKDGRFIV TPPLFAMKGK KENTLRILDA TNNQLPQDRE SLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT R VLENALVP ...String:
GVALGATRVI YPAGQKQVQL AVTNNDENST YLIQSWVENA DGVKDGRFIV TPPLFAMKGK KENTLRILDA TNNQLPQDRE SLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT R VLENALVP PMGESTVKLP SDAGSNITYR TINDYGALTP KMTGVMEHHH HHH

UniProtKB: Type 1 fimbria chaperone FimC

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Macromolecule #4: Type 1 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.081314 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG G CDVSARDV ...String:
FACKTANGTA IPIGGGSANV YVNLAPVVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSN FSGTVKYSGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG G CDVSARDV TVTLPDYPGS VPIPLTVYCA KSQNLGYYLS GTTADAGNSI FTNTASFSPA QGVGVQLTRN GTIIPANNTV SL GAVGTSA VSLGLTANYA RTGGQVTAGN VQSIIGVTFV YQ

UniProtKB: Type 1 fimbrin D-mannose specific adhesin

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.63 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3rfz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160422
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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