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- EMDB-50853: Cryo-EM structure of the type 1 pilus complex including pilus rod... -

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Basic information

Entry
Database: EMDB / ID: EMD-50853
TitleCryo-EM structure of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Map dataMap of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement (sharpened)
Sample
  • Complex: FimDHGFAnIChis complex
    • Protein or peptide: Fimbrin-like protein FimI
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Outer membrane usher protein FimD
Keywordsrod / pilus / usher / termination / MEMBRANE PROTEIN
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
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 / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer membrane usher protein FimD / Chaperone protein FimC / Fimbrin-like protein FimI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBachmann P / Afanasyev P / Boehringer D / Glockshuber R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_201234 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJul 2, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50853.png

Downloads & links

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Map

FileDownload / File: emd_50853.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å		1.02 Å/pix.
x 300 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.22550723 - 0.40001053
Average (Standard dev.)0.000865337 (±0.010592234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 pilus complex including...

Fileemd_50853_additional_1.map
AnnotationMap of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of the type 1 pilus complex...

Fileemd_50853_half_map_1.map
AnnotationHalf-map A of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the type 1 pilus complex...

Fileemd_50853_half_map_2.map
AnnotationHalf-map B of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnIChis complex

EntireName: FimDHGFAnIChis complex
Components
  • Complex: FimDHGFAnIChis complex
    • Protein or peptide: Fimbrin-like protein FimI
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Outer membrane usher protein FimD

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Supramolecule #1: FimDHGFAnIChis complex

SupramoleculeName: FimDHGFAnIChis complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Fimbrin-like protein FimI

MacromoleculeName: Fimbrin-like protein FimI / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.189334 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GNKWNTTLPG GNMQFQGVII AETCRIEAGD KQMTVNMGQI SSNRFHAVGE DSAPVPFVIH LRECSTVVSE RVGVAFHGVA DGKNPDVLS VGEGPGIATN IGVALFDDEG NLVPINRPPA NWKRLYSGST SLHFIAKYRA TGRRVTGGIA NAQAWFSLTY Q

UniProtKB: Fimbrin-like protein FimI

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Macromolecule #2: Chaperone protein FimC

MacromoleculeName: Chaperone protein FimC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.714109 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVK AIPSMDKSKL TENTLQLAII SRIKLYYRPA KLALPPDQAA EKLRFRRSAN SLTLINPTPY YLTVTELNAG T RVLENALV ...String:
MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVK AIPSMDKSKL TENTLQLAII SRIKLYYRPA KLALPPDQAA EKLRFRRSAN SLTLINPTPY YLTVTELNAG T RVLENALV PPMGESTVKL PSDAGSNITY RTINDYGALT PKMTGVMEHH HHHH

UniProtKB: Chaperone protein FimC

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Macromolecule #3: Outer membrane usher protein FimD

MacromoleculeName: Outer membrane usher protein FimD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 93.092805 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 ECRLVPRGSW SHPQFEK

UniProtKB: Outer membrane usher protein FimD

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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 R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average exposure time: 0.6 sec. / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41257
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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