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- EMDB-8954: Handover mechanism of the growing pilus by the bacterial outer me... -

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Basic information

Entry
Database: EMDB / ID: EMD-8954
TitleHandover mechanism of the growing pilus by the bacterial outer membrane usher FimD
Map data
Sample
  • Complex: FimDCFGH tip complex
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Fimbrial biogenesis outer membrane usher protein
    • Protein or peptide: Protein FimF
    • Protein or peptide: Protein FimG
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
Keywordspili / chaperone / usher / MEMBRANE 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 / : / protein folding chaperone / 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
Fimbrial biogenesis outer membrane usher protein / Protein FimF / Protein FimG / Type 1 fimbrin D-mannose specific adhesin / Outer membrane usher protein FimD / Chaperone protein FimC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsDu M / Yuan Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM062987 United States
CitationJournal: Nature / Year: 2018
Title: Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD.
Authors: Minge Du / Zuanning Yuan / Hongjun Yu / Nadine Henderson / Samema Sarowar / Gongpu Zhao / Glenn T Werneburg / David G Thanassi / Huilin Li /
Abstract: Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone- ...Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone-usher pathway. The outer-membrane usher FimD recruits pilus subunits bound by the chaperone FimC via the periplasmic N-terminal domain of the usher. Subunit translocation through the β-barrel channel of the usher occurs at the two C-terminal domains (which we label CTD1 and CTD2) of this protein. How the chaperone-subunit complex bound to the N-terminal domain is handed over to the C-terminal domains, as well as the timing of subunit polymerization into the growing pilus, have previously been unclear. Here we use cryo-electron microscopy to capture a pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH) in a conformation in which FimD is in the process of handing over the chaperone-bound end of the growing pilus to the C-terminal domains. In this structure, FimF has already polymerized with FimG, and the N-terminal domain of FimD swings over to bind CTD2; the N-terminal domain maintains contact with FimC-FimF, while at the same time permitting access to the C-terminal domains. FimD has an intrinsically disordered N-terminal tail that precedes the N-terminal domain. This N-terminal tail folds into a helical motif upon recruiting the FimC-subunit complex, but reorganizes into a loop to bind CTD2 during handover. Because both the N-terminal and C-terminal domains of FimD are bound to the end of the growing pilus, the structure further suggests a mechanism for stabilizing the assembly intermediate to prevent the pilus fibre diffusing away during the incorporation of thousands of subunits.
History
DepositionJul 9, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseOct 17, 2018-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6e15
  • Surface level: 0.0322
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8954.png

Downloads & links

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Map

FileDownload / File: emd_8954.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214.8 Å		1.07 Å/pix.
x 200 pix.
= 214.8 Å		1.07 Å/pix.
x 200 pix.
= 214.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0322 / Movie #1: 0.0322
Minimum - Maximum-0.0339591 - 0.07368164
Average (Standard dev.)0.0014776294 (±0.006009053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z214.800214.800214.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0340.0740.001

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Supplemental data

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Sample components

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Entire : FimDCFGH tip complex

EntireName: FimDCFGH tip complex
Components
  • Complex: FimDCFGH tip complex
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Fimbrial biogenesis outer membrane usher protein
    • Protein or peptide: Protein FimF
    • Protein or peptide: Protein FimG
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin

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Supramolecule #1: FimDCFGH tip complex

SupramoleculeName: FimDCFGH tip complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Chaperone protein FimC

MacromoleculeName: Chaperone protein FimC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.716869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNKNVNVRK SQEITFCLLA GILMFMAMMV AGRAEAGVAL GATRVIYPAG QKQEQLAVTN NDENSTYLIQ SWVENADGVK DGRFIVTPP LFAMKGKKEN TLRILDATNN QLPQDRESLF WMNVKAIPSM DKSKLTENTL QLAIISRIKL YYRPAKLALP P DQAAEKLR ...String:
MSNKNVNVRK SQEITFCLLA GILMFMAMMV AGRAEAGVAL GATRVIYPAG QKQEQLAVTN NDENSTYLIQ SWVENADGVK DGRFIVTPP LFAMKGKKEN TLRILDATNN QLPQDRESLF WMNVKAIPSM DKSKLTENTL QLAIISRIKL YYRPAKLALP P DQAAEKLR FRRSANSLTL INPTPYYLTV TELNAGTRVL ENALVPPMGE STVKLPSDAG SNITYRTIND YGALTPKMTG VM E

UniProtKB: Chaperone protein FimC

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Macromolecule #2: Fimbrial biogenesis outer membrane usher protein

MacromoleculeName: Fimbrial biogenesis outer membrane usher protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 96.705109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSYLNLRLYQ RNTQCLHIRK HRLAGFFVRL FVACAFAAQA SLSSAELYFN PRFLADDPQA VADLSRFENG QELPPGTYRV DIYLNNGYM ATRDVTFNTG DSEQGIVPCL TRAQLASMGL NTASVAGMNL LADDACVPLT TMVQDATAHL DVGQQRLNLT I PQAFMSNR ...String:
MSYLNLRLYQ RNTQCLHIRK HRLAGFFVRL FVACAFAAQA SLSSAELYFN PRFLADDPQA VADLSRFENG QELPPGTYRV DIYLNNGYM ATRDVTFNTG DSEQGIVPCL TRAQLASMGL NTASVAGMNL LADDACVPLT TMVQDATAHL DVGQQRLNLT I PQAFMSNR ARGYIPPELW DPGINAGLLN YNFSGNSVQN RIGGNSHYAY LNLQSGLNIG AWRLRDNTTW SYNSSDRSSG SK NKWQHIN TWLERDIIPL RSRLTLGDGY TQGDIFDGIN FRGAQLASDD NMLPDSQRGF APVIHGIARG TAQVTIKQNG YDI YNSTVP PGPFTINDIY AAGNSGDLQV TIKEADGSTQ IFTVPYSSVP LLQREGHTRY SITAGEYRSG NAQQEKPRFF QSTL LHGLP AGWTIYGGTQ LADRYRAFNF GIGKNMGALG ALSVDMTQAN STLPDDSQHD GQSVRFLYNK SLNESGTNIQ LVGYR YSTS GYFNFADTTY SRMNGYNIET QDGVIQVKPK FTDYYNLAYN KRGKLQLTVT QQLGRTSTLY LSGSHQTYWG TSNVDE QFQ AGLNTAFEDI NWTLSYSLTK NAWQKGRDQM LALNVNIPFS HWLRSDSKSQ WRHASASYSM SHDLNGRMTN LAGVYGT LL EDNNLSYSVQ TGYAGGGDGN SGSTGYATLN YRGGYGNANI GYSHSDDIKQ LYYGVSGGVL AHANGVTLGQ PLNDTVVL V KAPGAKDAKV ENQTGVRTDW RGYAVLPYAT EYRENRVALD TNTLADNVDL DNAVANVVPT RGAIVRAEFK ARVGIKLLM TLTHNNKPLP FGAMVTSESS QSSGIVADNG QVYLSGMPLA GKVQVKWGEE ENAHCVANYQ LPPESQQQLL TQLSAECRS

UniProtKB: Fimbrial biogenesis outer membrane usher protein

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Macromolecule #3: Protein FimF

MacromoleculeName: Protein FimF / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.379371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAADSTITIR GYVRDNGCSV AAESTNFTVD LMENAAKQFN NIGATTPVVP FRILLSPCGN AVSAVKVGFT GVADSHNANL LALENTVSA ASGLGIQLLN EQQNQIPLNA PSSALSWTTL TPGKPNTLNF YARLMATQVP VTAGHINATA TFTLEYQ

UniProtKB: Protein FimF

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Macromolecule #4: Protein FimG

MacromoleculeName: Protein FimG / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.190834 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAAILALASA TIQAADVTIT VNGKVVAKPC TVSTTNATVD LGDLYSFSLM SAGAASAWHD VALELTNCPV GTSRVTASFS GAADSTGYY KNQGTAQNIQ LELQDDSGNT LNTGATKTVQ VDDSSQSAHF PLQVRALTVN GGATQGTIQA VISITYTYS

UniProtKB: Protein FimG

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Macromolecule #5: Type 1 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.48826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN IYANNDVVVP TGGCDVSARD VTVTLPDYPG SVPIPLTVYC AKSQNLGYYL SGTTADAGNS IFTNTASFSP AQ GVGVQLT RNGTIIPANN TVSLGAVGTS AVSLGLTANY ARTGGQVTAG NVQSIIGVTF VYQ

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166913
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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