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- EMDB-50812: Cryo-EM map of the type 1 pilus complex including pilus rod and F... -

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Basic information

Entry
Database: EMDB / ID: EMD-50812
TitleCryo-EM map of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits
Map dataMap of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits (sharpened)
Sample
  • Complex: FimDHGFAnIChis
    • Protein or peptide: Type-1 fimbrial protein, A chain
    • Protein or peptide: Fimbrin-like protein FimI
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Outer membrane usher protein FimD
Keywordschaperone / usher / pilus / 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 / cell adhesion / identical protein binding
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
Type-1 fimbrial protein, A chain / 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: 4.3 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 map of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJun 27, 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_50812.png

Downloads & links

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Map

FileDownload / File: emd_50812.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 (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: 0.09
Minimum - Maximum-0.253522 - 0.4259526
Average (Standard dev.)0.0008646068 (±0.010255261)
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_50812_additional_1.map
AnnotationMap of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits (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_50812_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
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_50812_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
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

EntireName: FimDHGFAnIChis
Components
  • Complex: FimDHGFAnIChis
    • Protein or peptide: Type-1 fimbrial protein, A chain
    • 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

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

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Macromolecule #1: Type-1 fimbrial protein, A chain

MacromoleculeName: Type-1 fimbrial protein, A chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAATTVNGGT VHFKGEVVNA ACAVDAGSVD QTVQLGQVRT ASLAQEGATS SAVGFNIQLN DCDTNVASKA AVAFLGTAID AGHTNVLALQ SSAAGSATNV GVQILDRTGA ALTLDGATFS SETTLNNGTN TIPFQARYFA TGAATPGAAN ADATFKVQYQ

UniProtKB: Type-1 fimbrial protein, A chain

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Macromolecule #2: Fimbrin-like protein FimI

MacromoleculeName: Fimbrin-like protein FimI / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GNKWNTTLPG GNMQFQGVII AETCRIEAGD KQMTVNMGQI SSNRFHAVGE DSAPVPFVIH LRECSTVVSE RVGVAFHGVA DGKNPDVLSV GEGPGIATNI GVALFDDEGN LVPINRPPAN WKRLYSGSTS LHFIAKYRAT GRRVTGGIAN AQAWFSLTYQ

UniProtKB: Fimbrin-like protein FimI

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Macromolecule #3: Chaperone protein FimC

MacromoleculeName: Chaperone protein FimC / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT RVLENALVPP ...String:
MGVALGATRV IYPAGQKQEQ LAVTNNDENS TYLIQSWVEN ADGVKDGRFI VTPPLFAMKG KKENTLRILD ATNNQLPQDR ESLFWMNVKA IPSMDKSKLT ENTLQLAIIS RIKLYYRPAK LALPPDQAAE KLRFRRSANS LTLINPTPYY LTVTELNAGT RVLENALVPP MGESTVKLPS DAGSNITYRT INDYGALTPK MTGVMEHHHH HH

UniProtKB: Chaperone protein FimC

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Macromolecule #4: Outer membrane usher protein FimD

MacromoleculeName: Outer membrane usher protein FimD / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDAC VPLTTMVQDA TAHLDVGQQR LNLTIPQAFM SNRARGYIPP ELWDPGINAG LLNYNFSGNS VQNRIGGNSH YAYLNLQSGL ...String:
DLYFNPRFLA DDPQAVADLS RFENGQELPP GTYRVDIYLN NGYMATRDVT FNTGDSEQGI VPCLTRAQLA SMGLNTASVA GMNLLADDAC VPLTTMVQDA TAHLDVGQQR LNLTIPQAFM SNRARGYIPP ELWDPGINAG LLNYNFSGNS VQNRIGGNSH YAYLNLQSGL NIGAWRLRDN TTWSYNSSDR SSGSKNKWQH INTWLERDII PLRSRLTLGD GYTQGDIFDG INFRGAQLAS DDNMLPDSQR GFAPVIHGIA RGTAQVTIKQ NGYDIYNSTV PPGPFTINDI YAAGNSGDLQ VTIKEADGST QIFTVPYSSV PLLQREGHTR YSITAGEYRS GNAQQEKPRF FQSTLLHGLP AGWTIYGGTQ LADRYRAFNF GIGKNMGALG ALSVDMTQAN STLPDDSQHD GQSVRFLYNK SLNESGTNIQ LVGYRYSTSG YFNFADTTYS RMNGYNIETQ DGVIQVKPKF TDYYNLAYNK RGKLQLTVTQ QLGRTSTLYL SGSHQTYWGT SNVDEQFQAG LNTAFEDINW TLSYSLTKNA WQKGRDQMLA LNVNIPFSHW LRSDSKSQWR HASASYSMSH DLNGRMTNLA GVYGTLLEDN NLSYSVQTGY AGGGDGNSGS TGYATLNYRG GYGNANIGYS HSDDIKQLYY GVSGGVLAHA NGVTLGQPLN DTVVLVKAPG AKDAKVENQT GVRTDWRGYA VLPYATEYRE NRVALDTNTL ADNVDLDNAV ANVVPTRGAI VRAEFKARVG IKLLMTLTHN NKPLPFGAMV TSESSQSSGI VADNGQVYLS GMPLAGKVQV 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
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: 4.3 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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