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- EMDB-46596: Cryo-EM structure of E. coli FimH lectin domain bound to Fabs 440... -

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Basic information

Entry
Database: EMDB / ID: EMD-46596
TitleCryo-EM structure of E. coli FimH lectin domain bound to Fabs 440-2 and 454-3
Map data
Sample
  • Complex: FimH-DSG TM in complex with Fabs 440-2 and 445-3
    • Complex: FimH-DSG TM
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand complemented with FimG peptide 'triple mutant'
    • Complex: Fab 440-2
      • Protein or peptide: 440-2 Fab light chain
      • Protein or peptide: 440-2 Fab heavy chain
    • Complex: Fab 445-3
      • Protein or peptide: 445-3 Fab heavy chain
      • Protein or peptide: 445-3 Fab light chain
KeywordsAntigen / complex / adhesion / STRUCTURAL PROTEIN / CELL ADHESION / SUGAR BINDING PROTEIN
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: 4.24 Å
AuthorsLees JA / Han S
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
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
DepositionAug 15, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46596.png

Downloads & links

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Map

FileDownload / File: emd_46596.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.5587733 - 0.7621381
Average (Standard dev.)0.000013076372 (±0.014696463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46596_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_46596_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : FimH-DSG TM in complex with Fabs 440-2 and 445-3

EntireName: FimH-DSG TM in complex with Fabs 440-2 and 445-3
Components
  • Complex: FimH-DSG TM in complex with Fabs 440-2 and 445-3
    • Complex: FimH-DSG TM
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin FimH, Donor strand complemented with FimG peptide 'triple mutant'
    • Complex: Fab 440-2
      • Protein or peptide: 440-2 Fab light chain
      • Protein or peptide: 440-2 Fab heavy chain
    • Complex: Fab 445-3
      • Protein or peptide: 445-3 Fab heavy chain
      • Protein or peptide: 445-3 Fab light chain

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Supramolecule #1: FimH-DSG TM in complex with Fabs 440-2 and 445-3

SupramoleculeName: FimH-DSG TM in complex with Fabs 440-2 and 445-3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FimH-DSG TM

SupramoleculeName: FimH-DSG TM / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Fab 440-2

SupramoleculeName: Fab 440-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Fab 445-3

SupramoleculeName: Fab 445-3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: 440-2 Fab light chain

MacromoleculeName: 440-2 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.367045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPDIVMTQAA FSNPVTLGTS ASISCSSSKS LLHSNGITYL YWYLQRPGQS PQLLIYRMSN LASGVPDRFS GSGSGTDFAL RISRVETED VGVYYCAQML ERPYTFGSGT KLEIKRADAA PTVSIFPPSS EQLTSGGASV VCFLNNFYPK DINVKWKIDG S ERQNGVLN ...String:
SPDIVMTQAA FSNPVTLGTS ASISCSSSKS LLHSNGITYL YWYLQRPGQS PQLLIYRMSN LASGVPDRFS GSGSGTDFAL RISRVETED VGVYYCAQML ERPYTFGSGT KLEIKRADAA PTVSIFPPSS EQLTSGGASV VCFLNNFYPK DINVKWKIDG S ERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFNR NEC

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Macromolecule #2: 440-2 Fab heavy chain

MacromoleculeName: 440-2 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.603318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPQVQLTQSG AELVKPGASV KISCKASGYT FTDYYINWVK QRPGQGLEWI GKIGPGNNST YYKENFEGKA TLTADKSFST AYMQLSSLT SEDSAVYFCA RWGYLWSTGG GFDYWGHGTT LTVSSAKTTA PSVYPLAPVC GDTTGSSVTL GCLVKGYFPE P VTLTWNSG ...String:
SPQVQLTQSG AELVKPGASV KISCKASGYT FTDYYINWVK QRPGQGLEWI GKIGPGNNST YYKENFEGKA TLTADKSFST AYMQLSSLT SEDSAVYFCA RWGYLWSTGG GFDYWGHGTT LTVSSAKTTA PSVYPLAPVC GDTTGSSVTL GCLVKGYFPE P VTLTWNSG SLSSGVHTFP AVLQSDLYTL SSSVTVTSST WPSQSITCNV AHPASSTKVD KKIGGGHHHH HH

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Macromolecule #3: 445-3 Fab heavy chain

MacromoleculeName: 445-3 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.124822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPQVQLQQSG SELAKPGASV KLSCKASGYT FTRYWMHWVK QRPGQGLEWI GYSNPSSGYT NFNQKFKDKA ALTADTSSNT AYIQLNGLT FEDSAVYFCA RDGDPPFVYW GQGTLVTVSA AKTTAPSVYP LAPVCGDTTG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG ...String:
SPQVQLQQSG SELAKPGASV KLSCKASGYT FTRYWMHWVK QRPGQGLEWI GYSNPSSGYT NFNQKFKDKA ALTADTSSNT AYIQLNGLT FEDSAVYFCA RDGDPPFVYW GQGTLVTVSA AKTTAPSVYP LAPVCGDTTG SSVTLGCLVK GYFPEPVTLT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VTSSTWPSQS ITCNVAHPAS STKVDKKIGG GHHHHHH

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Macromolecule #4: 445-3 Fab light chain

MacromoleculeName: 445-3 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.696984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPDIQMTQSP ASLSASVGET VTITCRASEN IYSNLAWYQQ KQGKSPQLLV DGATNLADGV PSRFSGSGSG TQFSLKINSV QSEDFGNYY CQHFYGTPFT FGTGTKLEMK RADAAPTVSI FPPSSEQLTS GGASVVCFLN NFYPKDINVK WKIDGSERQN G VLNSWTDQ ...String:
SPDIQMTQSP ASLSASVGET VTITCRASEN IYSNLAWYQQ KQGKSPQLLV DGATNLADGV PSRFSGSGSG TQFSLKINSV QSEDFGNYY CQHFYGTPFT FGTGTKLEMK RADAAPTVSI FPPSSEQLTS GGASVVCFLN NFYPKDINVK WKIDGSERQN G VLNSWTDQ DSKDSTYSMS STLTLTKDEY ERHNSYTCEA THKTSTSPIV KSFNRNEC

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Macromolecule #5: 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: 5 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185595
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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