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- EMDB-45456: CryoEM Structure of Escherichia coli FimCH in complex with 2H04 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-45456
TitleCryoEM Structure of Escherichia coli FimCH in complex with 2H04 Fab
Map data
Sample
  • Complex: Complex of FimCH with 2H04 Fab
    • Organelle or cellular component: 2H04 Fab
      • Protein or peptide: 2H04 Fab light chain
      • Protein or peptide: 2H04 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: 3.17 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_45456.png

Downloads & links

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Map

FileDownload / File: emd_45456.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.)
0.84 Å/pix.
x 256 pix.
= 215.552 Å		0.84 Å/pix.
x 256 pix.
= 215.552 Å		0.84 Å/pix.
x 256 pix.
= 215.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0017718382 - 1.9657011
Average (Standard dev.)0.0007584034 (±0.019324882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45456_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_45456_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 2H04 Fab

EntireName: Complex of FimCH with 2H04 Fab
Components
  • Complex: Complex of FimCH with 2H04 Fab
    • Organelle or cellular component: 2H04 Fab
      • Protein or peptide: 2H04 Fab light chain
      • Protein or peptide: 2H04 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 2H04 Fab

SupramoleculeName: Complex of FimCH with 2H04 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #2: 2H04 Fab

SupramoleculeName: 2H04 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 / Details: FimH from UTI89 / 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: 2H04 Fab light chain

MacromoleculeName: 2H04 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.886432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSQIVLT QSPALMAASP GEKVTITCSV SSSISSSNLH WYQQKSETSP KPWIYGTSNL ASGVPIRFSG SGSGTSYSLT ISSLEAEDA ATYYCQQWRS YPWTFGGGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
TGVHSQIVLT QSPALMAASP GEKVTITCSV SSSISSSNLH WYQQKSETSP KPWIYGTSNL ASGVPIRFSG SGSGTSYSLT ISSLEAEDA ATYYCQQWRS YPWTFGGGTK LEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: 2H04 Fab heavy chain

MacromoleculeName: 2H04 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.400484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TGVHSEVQLQ QSGAELVKPG ASVKLSCKAS GYTFTSYWMH WVKQRPGQGL EWIGLIHPNS SSTYYNEKFK TRATLTVDKS SSTAYMQLS SLTSEDSAVY YCARLGYGNS YWYFDVWGTG TTVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
TGVHSEVQLQ QSGAELVKPG ASVKLSCKAS GYTFTSYWMH WVKQRPGQGL EWIGLIHPNS SSTYYNEKFK TRATLTVDKS SSTAYMQLS SLTSEDSAVY YCARLGYGNS YWYFDVWGTG 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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMHEPES
50.0 mMsodium chlorideNaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143176
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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