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- PDB-9me5: Antibody fragments from mAb824 and mAb926 bound to the adhesin pr... -

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Basic information

Entry
Database: PDB / ID: 9me5
TitleAntibody fragments from mAb824 and mAb926 bound to the adhesin protein FimH
Components
  • Protein FimG
  • Type 1 fimbrin D-mannose specific adhesin
  • mAb824 Heavy Chain Fragment
  • mAb824 Light Chain Fragment
  • mAb926 Heavy Chain Fragment
  • mAb926 Light Chain Fragment
KeywordsCELL ADHESION/IMMUNE SYSTEM / Fimbrial tip / Lectin domain / Antibody fragments / Antibody-target complex / CELL ADHESION / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHvorecny, K.L. / Magala, P. / Klevit, R.E. / Kollman, J.M.
Funding support United States, 4items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 1 fimbrin D-mannose specific adhesin
G: Protein FimG
H: mAb926 Heavy Chain Fragment
I: mAb824 Heavy Chain Fragment
L: mAb926 Light Chain Fragment
M: mAb824 Light Chain Fragment


Theoretical massNumber of molelcules
Total (without water)140,0276
Polymers140,0276
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Type 1 fimbrin D-mannose specific adhesin / Protein FimH


Mass: 31488.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191
#2: Protein Protein FimG


Mass: 17328.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimG, b4319, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190

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Antibody , 4 types, 4 molecules HILM

#3: Antibody mAb926 Heavy Chain Fragment


Mass: 22703.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma
#4: Antibody mAb824 Heavy Chain Fragment


Mass: 22526.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma
#5: Antibody mAb926 Light Chain Fragment


Mass: 24222.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma
#6: Antibody mAb824 Light Chain Fragment


Mass: 21757.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: B cell hybridoma

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimHCOMPLEXall0MULTIPLE SOURCES
2Fimbrial tip (FimH and FimG)COMPLEX#1-#21RECOMBINANT
3Antibody Fragments, Heavy and Light ChainsCOMPLEX#3-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDTissue
12Escherichia coli (E. coli)562
23Mus musculus (house mouse)10090B cell
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails
1142GATAN K3 BIOQUANTUM (6k x 4k)115349SerialEM
2155GATAN K3 BIOQUANTUM (6k x 4k)11651Leginon

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253258 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13JWN

3jwn

13JWN1PDBexperimental model
215C8

15c8

115C82PDBexperimental model
RefinementCross valid method: NONE

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