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- EMDB-48187: Antibody fragments from mAb21 and mAb475 bound to the fimbrial ti... -

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Entry
Database: EMDB / ID: EMD-48187
TitleAntibody fragments from mAb21 and mAb475 bound to the fimbrial tip protein, FimH
Map dataAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Sample
  • Complex: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
    • Complex: Fimbrial tip
      • Protein or peptide: FimH
      • Protein or peptide: FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb475 Heavy Chain Fragment
      • Protein or peptide: mAb475 Light Chain Fragment
      • Protein or peptide: mAb21 Heavy Chain Fragment
      • Protein or peptide: mAb21 Light Chain Fragment
KeywordsFimbrial tip / Lectin domain / Antibody fragments / Antibody-target complex / CELL ADHESION
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsHvorecny KL / Magala P / Klevit RE / Kollman JM
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM149542 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI145111 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI171570 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99 GM141364 United States
CitationJournal: Nat Commun / Year: 2025
Title: Antibodies disrupt bacterial adhesion by ligand mimicry and allosteric interference.
Authors: Kelli L Hvorecny / Gianluca Interlandi / Tim S Veth / Pavel Aprikian / Anna Manchenko / Veronika L Tchesnokova / Miles S Dickinson / Joel D Quispe / Nicholas M Riley / Rachel E Klevit / ...Authors: Kelli L Hvorecny / Gianluca Interlandi / Tim S Veth / Pavel Aprikian / Anna Manchenko / Veronika L Tchesnokova / Miles S Dickinson / Joel D Quispe / Nicholas M Riley / Rachel E Klevit / Pearl Magala / Evgeni V Sokurenko / Justin M Kollman /
Abstract: A critical step in infections is the attachment of microorganisms to host cells using lectins that bind glycans, making lectins promising antimicrobial targets. Upon binding mannosylated glycans, ...A critical step in infections is the attachment of microorganisms to host cells using lectins that bind glycans, making lectins promising antimicrobial targets. Upon binding mannosylated glycans, FimH, an adhesin in E. coli, undergoes an allosteric transition from an inactive to an active conformation that can act as a catch-bond. Distinct monoclonal antibodies that alter FimH glycan binding are available, but the mechanisms of action remain unclear. Here, we use cryo-electron microscopy, mass spectrometry, adhesion assays, and molecular dynamics simulations to determine the structure-function relationships underlying antibody-FimH binding. Our study demonstrates four mechanisms of action: ligand mimicry by an N-linked, high-mannose glycan; stabilization of the ligand pocket in the inactive state; conformational trapping of the active and inactive states; and locking of the ligand pocket through long-range allosteric effects. These structures reveal multiple mechanisms of antibody responses to an allosteric protein and provide blueprints for antimicrobials that target adhesins.
History
DepositionDec 6, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48187.png

Downloads & links

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Map

FileDownload / File: emd_48187.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 320 pix.
= 569.6 Å		1.78 Å/pix.
x 320 pix.
= 569.6 Å		1.78 Å/pix.
x 320 pix.
= 569.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.44256762 - 1.1065748
Average (Standard dev.)-0.00046276118 (±0.016919153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 569.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_1.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1 with gaussian filter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_2.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2 with gaussian filter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map of antibody fragments from mAb21 and...

Fileemd_48187_additional_3.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map of antibody fragments from mAb21 and...

Fileemd_48187_additional_4.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_5.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of antibody fragments from mAb21 and...

Fileemd_48187_half_map_1.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of antibody fragments from mAb21 and...

Fileemd_48187_half_map_2.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody fragments from mAb21 and mAb475 bound to the fimbrial ti...

EntireName: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
Components
  • Complex: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
    • Complex: Fimbrial tip
      • Protein or peptide: FimH
      • Protein or peptide: FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb475 Heavy Chain Fragment
      • Protein or peptide: mAb475 Light Chain Fragment
      • Protein or peptide: mAb21 Heavy Chain Fragment
      • Protein or peptide: mAb21 Light Chain Fragment

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Supramolecule #1: Antibody fragments from mAb21 and mAb475 bound to the fimbrial ti...

SupramoleculeName: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fimbrial tip

SupramoleculeName: Fimbrial tip / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Antibody Fragments

SupramoleculeName: Antibody Fragments / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma

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Macromolecule #1: FimH

MacromoleculeName: FimH / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDY PETITDYVTL QRGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR T DKPWPVAL YLTPVSSAGG VAIKAGSLIA VLILRQTNNY NSDDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDY PETITDYVTL QRGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR T DKPWPVAL YLTPVSSAGG VAIKAGSLIA VLILRQTNNY NSDDFQFVWN IYANNDVVVP TG GCDVSAR DVTVTLPDYP GSVPIPLTVY CAKSQNLGYY LSGTTADAGN SIFTNTASFS PAQ GVGVQL TRNGTIIPAN NTVSLGAVGT SAVSLGLTAN YARTGGQVTA GNVQSIIGVT FVYQ

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Macromolecule #2: FimG

MacromoleculeName: FimG / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKWCKRGYVL AAILALASAT IQAADVTITV NGKVVAKPCT VSTTNATVDL GDLYSFSLMS AGAASAWHD VALELTNCPV GTSRVTASFS GAADSTGYYK NQGTAQNIQL ELQDDSGNTL N TGATKTVQ VDDSSQSAHF PLQVRALTVN GGATQGTIQA VISITYTYS

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Macromolecule #3: mAb475 Heavy Chain Fragment

MacromoleculeName: mAb475 Heavy Chain Fragment / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: QVQLQQSGAE LVRPGSSVKI SCKASGYAFS SYWMNWVKQR PGQGLEWIGQ IYPRDGDTNY NGKFMDKVTL TADKSSNTAY MQLSSLTSED SAVYFCEVGR GFYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGSLSSGVHT ...String:
QVQLQQSGAE LVRPGSSVKI SCKASGYAFS SYWMNWVKQR PGQGLEWIGQ IYPRDGDTNY NGKFMDKVTL TADKSSNTAY MQLSSLTSED SAVYFCEVGR GFYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVPS SPRPSETVTC NVAHPASSTK VDKKI

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Macromolecule #4: mAb475 Light Chain Fragment

MacromoleculeName: mAb475 Light Chain Fragment / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: ELQMTQSPKF MSTSVGDRVS VTCKASQNVS NVAWYQQKPG QSPKAMIYSA SYRYSGVPGR FTGSGSGTDF TLTINNVQSE DLATYFCQQN SSFPFTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS ...String:
ELQMTQSPKF MSTSVGDRVS VTCKASQNVS NVAWYQQKPG QSPKAMIYSA SYRYSGVPGR FTGSGSGTDF TLTINNVQSE DLATYFCQQN SSFPFTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFNR NEC

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Macromolecule #5: mAb21 Heavy Chain Fragment

MacromoleculeName: mAb21 Heavy Chain Fragment / type: protein_or_peptide / ID: 5 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: EVLLKQSGPE KVKPGASVKI PCKASGYTFT DYNIDWVKQS HGTSLEWIGH LDPNSGGTVY NQKFRGKATL TVDKSSSTAY LELRSLTSED TAVYYCARST MGVYRSDGYY AMDYWGQGTS VTVSSAKTTP PSVYPLAPGC GDTTGSSVTL GCLVKGYFPE SVTVTWNSGS ...String:
EVLLKQSGPE KVKPGASVKI PCKASGYTFT DYNIDWVKQS HGTSLEWIGH LDPNSGGTVY NQKFRGKATL TVDKSSSTAY LELRSLTSED TAVYYCARST MGVYRSDGYY AMDYWGQGTS VTVSSAKTTP PSVYPLAPGC GDTTGSSVTL GCLVKGYFPE SVTVTWNSGS LSSSVHTFPA LLQSGLYTMS SSVTVPSS

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Macromolecule #6: mAb21 Light Chain Fragment

MacromoleculeName: mAb21 Light Chain Fragment / type: protein_or_peptide / ID: 6 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString:
QIVLTQSPAI MSASLGEEIT LTCSASSSIS YMHWYQQKSG TSPKILIYST SNQASGVPSR FSGSGSGTFY SLTISSVEAE DAADYYCHQW SSYPWTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TK

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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: 7.4
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3222 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 188465
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.4.1)

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