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- EMDB-45460: CryoEM Structure of Escherichia coli FimCH in complex with 2C07 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-45460
TitleCryoEM Structure of Escherichia coli FimCH in complex with 2C07 Fab
Map data
Sample
  • Complex: Complex of FimCH with 2C07 Fab
    • Organelle or cellular component: 2C07 Fab
      • Protein or peptide: 2C07 light chain
      • Protein or peptide: 2C07 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: 3.69 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_45460.png

Downloads & links

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Map

FileDownload / File: emd_45460.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 303.104 Å		1.18 Å/pix.
x 256 pix.
= 303.104 Å		1.18 Å/pix.
x 256 pix.
= 303.104 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-0.0017126445 - 2.4301472
Average (Standard dev.)0.00049535534 (±0.017701933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 303.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45460_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45460_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 2C07 Fab

EntireName: Complex of FimCH with 2C07 Fab
Components
  • Complex: Complex of FimCH with 2C07 Fab
    • Organelle or cellular component: 2C07 Fab
      • Protein or peptide: 2C07 light chain
      • Protein or peptide: 2C07 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 2C07 Fab

SupramoleculeName: Complex of FimCH with 2C07 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: 2C07 Fab

SupramoleculeName: 2C07 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: 2C07 light chain

MacromoleculeName: 2C07 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.907457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSDIVMT QSQKFMSTSV GDRVSVTCKA SQNVVTNVAW YQQKSGQSPK VVIYSASFRS SGVPDRFTGS GSGTDFTLTI SNVQSEDLA EYFCHQYNSH PLTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
TGVHSDIVMT QSQKFMSTSV GDRVSVTCKA SQNVVTNVAW YQQKSGQSPK VVIYSASFRS SGVPDRFTGS GSGTDFTLTI SNVQSEDLA EYFCHQYNSH PLTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: 2C07 heavy chain

MacromoleculeName: 2C07 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.386527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSEVKLV ESGEGLVKPG GSLKLSCAAS GFTFSSYAMS WVRQTPEKRL DWVAYISSGG DHIYYADTVK GRFTISRDNA RNTLYLQMS SLKSEDTAMY YCTRDTGYYV SRYFDVWGTG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
TGVHSEVKLV ESGEGLVKPG GSLKLSCAAS GFTFSSYAMS WVRQTPEKRL DWVAYISSGG DHIYYADTVK GRFTISRDNA RNTLYLQMS SLKSEDTAMY YCTRDTGYYV SRYFDVWGTG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CRSLVPRGSS GH HHHHH

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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: 54.6 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: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210906
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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