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- EMDB-45458: CryoEM Structure of Escherichia coli FimCH in complex with F7 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-45458
TitleCryoEM Structure of Escherichia coli FimCH in complex with F7 Fab
Map data
Sample
  • Complex: Complex of FimCH with F7 Fab
    • Organelle or cellular component: F7 Fab
      • Protein or peptide: F7 Fab light chain
      • Protein or peptide: F7 Fab heavy chain
    • Organelle or cellular component: FimH adhesin in complex with FimC chaperone
      • Protein or peptide: Type 1 fimbiral adhesin FimH
KeywordsAdhesin / Inhibitor / complex / Fab / Chaperone / Usher / Pili / CELL ADHESION
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type 1 fimbiral adhesin FimH
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse) / Escherichia coli UTI89 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLopatto EDB / Hultgren SJ
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI157797 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165915 United States
CitationJournal: Sci Adv / Year: 2025
Title: Monoclonal antibodies targeting the FimH adhesin protect against uropathogenic UTI.
Authors: Edward D B Lopatto / Jesús M Santiago-Borges / Denise A Sanick / Sameer Kumar Malladi / Philippe N Azimzadeh / Morgan W Timm / Isabella F Fox / Aaron J Schmitz / Jackson S Turner / Shaza M ...Authors: Edward D B Lopatto / Jesús M Santiago-Borges / Denise A Sanick / Sameer Kumar Malladi / Philippe N Azimzadeh / Morgan W Timm / Isabella F Fox / Aaron J Schmitz / Jackson S Turner / Shaza M Sayed Ahmed / Lillian Ortinau / Nathaniel C Gualberto / Jerome S Pinkner / Karen W Dodson / Ali H Ellebedy / Andrew L Kau / Scott J Hultgren /
Abstract: As antimicrobial resistance increases, urinary tract infections (UTIs) are expected to pose an increased burden in morbidity and expense on the health care system, increasing the need for alternative ...As antimicrobial resistance increases, urinary tract infections (UTIs) are expected to pose an increased burden in morbidity and expense on the health care system, increasing the need for alternative antibiotic-sparing treatments. Most UTIs are caused by uropathogenic (UPEC), whereas causes a large portion of non-UPEC UTIs. Both bacteria express type 1 pili tipped with the mannose-binding FimH adhesin critical for UTI pathogenesis. We generated and biochemically characterized 33 murine monoclonal antibodies (mAbs) to FimH. Three mAbs protected mice from UTI. Mechanistically, we show that this protection is Fc independent and mediated by the ability of these mAbs to sterically block FimH function by recognizing a high-affinity FimH conformation. Our data reveal that FimH mAbs hold promise as an antibiotic-sparing treatment strategy.
History
DepositionJun 23, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45458.png

Downloads & links

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Map

FileDownload / File: emd_45458.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 208 pix.
= 246.272 Å		1.18 Å/pix.
x 208 pix.
= 246.272 Å		1.18 Å/pix.
x 208 pix.
= 246.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.184 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0017560109 - 2.3230376
Average (Standard dev.)0.00077597465 (±0.021506622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 246.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45458_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45458_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of FimCH with F7 Fab

EntireName: Complex of FimCH with F7 Fab
Components
  • Complex: Complex of FimCH with F7 Fab
    • Organelle or cellular component: F7 Fab
      • Protein or peptide: F7 Fab light chain
      • Protein or peptide: F7 Fab heavy chain
    • Organelle or cellular component: FimH adhesin in complex with FimC chaperone
      • Protein or peptide: Type 1 fimbiral adhesin FimH

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Supramolecule #1: Complex of FimCH with F7 Fab

SupramoleculeName: Complex of FimCH with F7 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: F7 Fab

SupramoleculeName: F7 Fab / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: FimH adhesin in complex with FimC chaperone

SupramoleculeName: FimH adhesin in complex with FimC chaperone / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1
Details: FimH adhesin expressed in complex with FimC chaperone
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Type 1 fimbiral adhesin FimH

MacromoleculeName: Type 1 fimbiral adhesin FimH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli UTI89 (bacteria)
Molecular weightTheoretical: 29.03726 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FACKTANGTA IPIGGGSANV YVNLAPAVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GAAYGGVLSS FSGTVKYNGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG G CDVSARDV ...String:
FACKTANGTA IPIGGGSANV YVNLAPAVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GAAYGGVLSS FSGTVKYNGS 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 fimbiral adhesin FimH

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Macromolecule #2: F7 Fab light chain

MacromoleculeName: F7 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.781291 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSQIVLT QSPALMAASP GEKVTITCSV SSSIGSSNLH WYQQKSETSP KPWIYGTSNL ASGVPVRFSG SGSGTSYSLT ISSMEAEDA ATYYCQQWST YPYTFGGGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
TGVHSQIVLT QSPALMAASP GEKVTITCSV SSSIGSSNLH WYQQKSETSP KPWIYGTSNL ASGVPVRFSG SGSGTSYSLT ISSMEAEDA ATYYCQQWST YPYTFGGGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: F7 Fab heavy chain

MacromoleculeName: F7 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.131266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSEVQLQ QPGPVLVKPG PSVKISCKAS GFTFTDYFIH WVKQSHGKSL EWIGLVSPYN GGTYYNQQFK GKATLTVDTS SSTAYMDLN SLTSEDSAVY YCTRLLRGYW YFDVWGTGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
TGVHSEVQLQ QPGPVLVKPG PSVKISCKAS GFTFTDYFIH WVKQSHGKSL EWIGLVSPYN GGTYYNQQFK GKATLTVDTS SSTAYMDLN SLTSEDSAVY YCTRLLRGYW YFDVWGTGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCR SLVPRGSSGH HH HHH

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
50.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129896
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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