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- EMDB-50861: Cryo-EM structure of the type 1 chaperone-usher pilus FimD-tip co... -

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Basic information

Entry
Database: EMDB / ID: EMD-50861
TitleCryo-EM structure of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1
Map dataMap of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1 (sharpened)
Sample
  • Complex: FimDHGFAnC complex
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Outer membrane usher protein FimD
    • Protein or peptide: Protein FimF
    • Protein or peptide: Protein FimG
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
Keywordschaperone / usher / pilus / tip / CELL ADHESION
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
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: 3.3 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 structure of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1
Authors: Bachmann P / Afanasyev P / Boehringer D / Glockshuber R
History
DepositionJul 3, 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_50861.png

Downloads & links

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Map

FileDownload / File: emd_50861.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1 (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 331.776 Å		1.3 Å/pix.
x 256 pix.
= 331.776 Å		1.3 Å/pix.
x 256 pix.
= 331.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-2.2412355 - 2.9625201
Average (Standard dev.)-0.00042229975 (±0.04322722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the type 1 chaperone-usher pilus FimD-tip...

Fileemd_50861_additional_1.map
AnnotationMap of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1 (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 chaperone-usher pilus...

Fileemd_50861_half_map_1.map
AnnotationHalf-map A of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1
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 chaperone-usher pilus...

Fileemd_50861_half_map_2.map
AnnotationHalf-map B of the type 1 chaperone-usher pilus FimD-tip complex (FimDHGFC) - Conformer 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FimDHGFAnC complex

EntireName: FimDHGFAnC complex
Components
  • Complex: FimDHGFAnC complex
    • Protein or peptide: Chaperone protein FimC
    • Protein or peptide: Outer membrane usher protein FimD
    • 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: FimDHGFAnC complex

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

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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: 22.885229 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 PKMTGVME

UniProtKB: Chaperone protein FimC

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Macromolecule #2: Outer membrane usher protein FimD

MacromoleculeName: Outer membrane usher protein FimD / type: protein_or_peptide / ID: 2 / 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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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: 16.177095 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 #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: 14.864227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADVTITVNGK VVAKPCTVST TNATVDLGDL YSFSLMSAGA ASAWHDVALE LTNCPVGTSR VTASFSGAAD STGYYKNQGT AQNIQLELQ DDSGNTLNTG ATKTVQVDDS SQSAHFPLQV RALTVNGGAT QGTIQAVISI TYTYS

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: 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
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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.1 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 242477
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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