9ME7 | pdb_00009me7

Antibody fragments from mAb21 and mAb824 bound to the adhesin protein FimH containing alpha-methyl mannose


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ME7

This is version 1.1 of the entry. See complete history

Literature

Antibodies disrupt bacterial adhesion by ligand mimicry and allosteric interference.

Hvorecny, K.L.Interlandi, G.Veth, T.S.Aprikian, P.Manchenko, A.Tchesnokova, V.L.Dickinson, M.S.Quispe, J.D.Riley, N.M.Klevit, R.E.Magala, P.Sokurenko, E.V.Kollman, J.M.

(2025) Nat Commun 16: 10590-10590

  • DOI: https://doi.org/10.1038/s41467-025-65666-3
  • Primary Citation Related Structures: 
    9ME4, 9ME5, 9ME6, 9ME7, 9PTM

  • PubMed 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, 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.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 116.85 kDa 
  • Atom Count: 7,196 
  • Modeled Residue Count: 943 
  • Deposited Residue Count: 1,085 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesin300Escherichia coliMutation(s): 0 
Gene Names: fimHb4320JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08191
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb824 Heavy Chain FragmentB [auth I]208Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb21 Heavy Chain FragmentC [auth J]198Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb824 Light Chain FragmentD [auth M]197Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb21 Light Chain FragmentE [auth N]182Mus musculusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMA
(Subject of Investigation/LOI)

Query on MMA



Download:Ideal Coordinates CCD File
F [auth A]methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM149542
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF32 AI145111
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01 AI171570
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99 GM141364

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references