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- EMDB-43048: Cryo-EM structure of E. coli FimH lectin domain bound to Fabs 329... -

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Basic information

Entry
Database: EMDB / ID: EMD-43048
TitleCryo-EM structure of E. coli FimH lectin domain bound to Fabs 329-2 and 454-3
Map data
Sample
  • Complex: Ternary complex of E. coli FimH with Fabs 329-2 and 454-3
    • Protein or peptide: Fab 329-2 heavy chain
    • Protein or peptide: Fab 454-3 heavy chain
    • Protein or peptide: Fab 329-2 light chain
    • Protein or peptide: Fab 454-3 light chain
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand complemented with FimG peptide 'triple mutant'
KeywordsBacterial proteins / lectin domain / Fab / urinary tract infections / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Protein FimG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsLees JA / Han S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2025
Title: Structure-based design of an immunogenic, conformationally stabilized FimH antigen for a urinary tract infection vaccine.
Authors: Natalie C Silmon de Monerri / Ye Che / Joshua A Lees / Jayasankar Jasti / Huixian Wu / Matthew C Griffor / Srinivas Kodali / Julio Cesar Hawkins / Jacqueline Lypowy / Christopher Ponce / ...Authors: Natalie C Silmon de Monerri / Ye Che / Joshua A Lees / Jayasankar Jasti / Huixian Wu / Matthew C Griffor / Srinivas Kodali / Julio Cesar Hawkins / Jacqueline Lypowy / Christopher Ponce / Kieran Curley / Alexandre Esadze / Juan Carcamo / Thomas McLellan / David Keeney / Arthur Illenberger / Yury V Matsuka / Suman Shanker / Laurent Chorro / Alexey V Gribenko / Seungil Han / Annaliesa S Anderson / Robert G K Donald /
Abstract: Adhesion of E. coli to the urinary tract epithelium is a critical step in establishing urinary tract infections. FimH is an adhesin positioned on the fimbrial tip which binds to mannosylated proteins ...Adhesion of E. coli to the urinary tract epithelium is a critical step in establishing urinary tract infections. FimH is an adhesin positioned on the fimbrial tip which binds to mannosylated proteins on the urinary tract epithelium via its lectin domain (FimHLD). FimH is of interest as a target of vaccines to prevent urinary tract infections (UTI). Previously, difficulties in obtaining purified recombinant FimH from E. coli along with the poor inherent immunogenicity of FimH have hindered the development of effective FimH vaccine candidates. To overcome these challenges, we have devised a novel production method using mammalian cells to produce high yields of homogeneous FimH protein with comparable biochemical and immunogenic properties to FimH produced in E. coli. Next, to optimize conformational stability and immunogenicity of FimH, we used a computational approach to design improved FimH mutants and evaluated their biophysical and biochemical properties, and murine immunogenicity using a bacterial adhesion inhibition assay. This approach identified an immunogenic FimH variant (FimH-donor-strand complemented with FimG peptide 'triple mutant', FimH-DSG TM) capable of blocking bacterial adhesion that is produced at high yields in mammalian cells. By x-ray crystallography, we confirmed that the stabilized structure of the FimHLD in FimH-DSG TM is similar to native FimH on the fimbrial tip. Characterization of monoclonal antibodies elicited by FimH-DSG that can block bacterial binding to mannosylated surfaces identified 4 non-overlapping binding sites whose epitopes were mapped via a combinatorial cryogenic electron microscopy approach. Novel inhibitory epitopes in the lectin binding FimH were identified, revealing diverse functional mechanisms of FimH-directed antibodies with relevance to FimH-targeted UTI vaccines.
History
DepositionDec 7, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43048.png

Downloads & links

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Map

FileDownload / File: emd_43048.map.gz / Format: CCP4 / Size: 54.1 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 242 pix.
= 285.56 Å		1.18 Å/pix.
x 242 pix.
= 285.56 Å		1.18 Å/pix.
x 242 pix.
= 285.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.5521271 - 2.675079
Average (Standard dev.)-0.0006264393 (±0.042346705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions242242242
Spacing242242242
CellA=B=C: 285.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43048_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_43048_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 : Ternary complex of E. coli FimH with Fabs 329-2 and 454-3

EntireName: Ternary complex of E. coli FimH with Fabs 329-2 and 454-3
Components
  • Complex: Ternary complex of E. coli FimH with Fabs 329-2 and 454-3
    • Protein or peptide: Fab 329-2 heavy chain
    • Protein or peptide: Fab 454-3 heavy chain
    • Protein or peptide: Fab 329-2 light chain
    • Protein or peptide: Fab 454-3 light chain
    • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand complemented with FimG peptide 'triple mutant'

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Supramolecule #1: Ternary complex of E. coli FimH with Fabs 329-2 and 454-3

SupramoleculeName: Ternary complex of E. coli FimH with Fabs 329-2 and 454-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #5, #3-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Fab 454-3 heavy chain

MacromoleculeName: Fab 454-3 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.940627 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QVQLQQSGSE LAKPGASVKL SCKASGYTFT RYWMHWVKQR PGQGLEWIGY SNPSSGYTNF NQKFKDKAAL TADTSSNTAY IQLNGLTFE DSAVYFCARD GDPPFVYWGQ GTLVTVSAAK TTAPSVYPLA PVCGDTTGSS VTLGCLVKGY FPEPVTLTWN S GSLSSGVH ...String:
QVQLQQSGSE LAKPGASVKL SCKASGYTFT RYWMHWVKQR PGQGLEWIGY SNPSSGYTNF NQKFKDKAAL TADTSSNTAY IQLNGLTFE DSAVYFCARD GDPPFVYWGQ GTLVTVSAAK TTAPSVYPLA PVCGDTTGSS VTLGCLVKGY FPEPVTLTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVT SSTWPSQSIT CNVAHPASST KVDKKIGGGH HHHHH

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Macromolecule #2: Fab 329-2 heavy chain

MacromoleculeName: Fab 329-2 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.103885 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVKLVESGGG LVKPGGSLKL SCTASGFTFS DNGMAWVRQV PGKGPEWVAS ITNLAFSVYY SDTVTGRFTI SRDNAKNTLA LEMSSLRSE DTAIYYCARL YGDYPYYFDY WGQGTALTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS ...String:
EVKLVESGGG LVKPGGSLKL SCTASGFTFS DNGMAWVRQV PGKGPEWVAS ITNLAFSVYY SDTVTGRFTI SRDNAKNTLA LEMSSLRSE DTAIYYCARL YGDYPYYFDY WGQGTALTVS SAKTTAPSVY PLAPVCGDTT GSSVTLGCLV KGYFPEPVTL T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIG GGHHHHHH

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Macromolecule #3: Fab 454-3 light chain

MacromoleculeName: Fab 454-3 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.512791 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIQMTQSPAS LSASVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVDG ATNLADGVPS RFSGSGSGTQ FSLKINSVQS EDFGNYYCQ HFYGTPFTFG TGTKLEMKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSPAS LSASVGETVT ITCRASENIY SNLAWYQQKQ GKSPQLLVDG ATNLADGVPS RFSGSGSGTQ FSLKINSVQS EDFGNYYCQ HFYGTPFTFG TGTKLEMKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #4: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand comp...

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand complemented with FimG peptide 'triple mutant'
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 32.118596 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: FACKTASGTA IPIGAASANV YVNLAPAVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSS FSGTVKYSGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG G CDVSARDV ...String:
FACKTASGTA IPIGAASANV YVNLAPAVNV GQNLVVDLST QIFCHNDYPE TITDYVTLQR GSAYGGVLSS FSGTVKYSGS SYPFPTTSE TPRVVYNSRT DKPWPVALYL TPVSSAGGVA IKAGSLIAVL ILRQTNNYNS DDFQFVWNIY ANNDVVVPTG G CDVSARDV TVTLPDYPGS VPIPLTVYCA KSQNLGYYLS GTTADAGNSI FTNTASFSPA QGVGVQLTRQ GTIIPANNTV SL GAVGTSA VSLGLTANYA RTGGQVTAGN VQSIIGVTFV YQGGSSGGGA DVTITVNGKV VAKGGHHHHH HHH

UniProtKB: Type 1 fimbrin D-mannose specific adhesin, Protein FimG

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Macromolecule #5: Fab 329-2 light chain

MacromoleculeName: Fab 329-2 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.611023 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVLTQSPAT LSVTPGESVS LFCRASQTIG NSLHWYQQKS HESPRLLIKY SSLSISGIPS RFSGSGSGTD FTLSINSVET EDFGVFFCQ QSHNWPITFG AGTKLELRRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVLTQSPAT LSVTPGESVS LFCRASQTIG NSLHWYQQKS HESPRLLIKY SSLSISGIPS RFSGSGSGTD FTLSINSVET EDFGVFFCQ QSHNWPITFG AGTKLELRRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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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

Concentration0.25 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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