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- PDB-9ccs: CryoEM Structure of Escherichia coli FimCH in complex with 2H04 Fab -

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Basic information

Entry
Database: PDB / ID: 9ccs
TitleCryoEM Structure of Escherichia coli FimCH in complex with 2H04 Fab
Components
  • 2H04 Fab heavy chain
  • 2H04 Fab light chain
  • Type 1 fimbiral adhesin FimH
KeywordsCELL ADHESION / Adhesin / Inhibitor / complex / Fab / Chaperone / Usher / Pili
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type 1 fimbiral adhesin FimH
Similarity search - Component
Biological speciesEscherichia coli UTI89 (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLopatto, E.D.B. / Hultgren, S.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI157797 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI165915 United States
CitationJournal: Sci Adv / Year: 2025
Title: Monoclonal antibodies targeting the FimH adhesin protect against uropathogenic UTI.
Authors: Edward D B Lopatto / Jesús M Santiago-Borges / Denise A Sanick / Sameer Kumar Malladi / Philippe N Azimzadeh / Morgan W Timm / Isabella F Fox / Aaron J Schmitz / Jackson S Turner / Shaza M ...Authors: Edward D B Lopatto / Jesús M Santiago-Borges / Denise A Sanick / Sameer Kumar Malladi / Philippe N Azimzadeh / Morgan W Timm / Isabella F Fox / Aaron J Schmitz / Jackson S Turner / Shaza M Sayed Ahmed / Lillian Ortinau / Nathaniel C Gualberto / Jerome S Pinkner / Karen W Dodson / Ali H Ellebedy / Andrew L Kau / Scott J Hultgren /
Abstract: As antimicrobial resistance increases, urinary tract infections (UTIs) are expected to pose an increased burden in morbidity and expense on the health care system, increasing the need for alternative ...As antimicrobial resistance increases, urinary tract infections (UTIs) are expected to pose an increased burden in morbidity and expense on the health care system, increasing the need for alternative antibiotic-sparing treatments. Most UTIs are caused by uropathogenic (UPEC), whereas causes a large portion of non-UPEC UTIs. Both bacteria express type 1 pili tipped with the mannose-binding FimH adhesin critical for UTI pathogenesis. We generated and biochemically characterized 33 murine monoclonal antibodies (mAbs) to FimH. Three mAbs protected mice from UTI. Mechanistically, we show that this protection is Fc independent and mediated by the ability of these mAbs to sterically block FimH function by recognizing a high-affinity FimH conformation. Our data reveal that FimH mAbs hold promise as an antibiotic-sparing treatment strategy.
History
DepositionJun 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type 1 fimbiral adhesin FimH
B: 2H04 Fab light chain
C: 2H04 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)79,3243
Polymers79,3243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Type 1 fimbiral adhesin FimH


Mass: 29037.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FimH from UTI89 / Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Gene: fimH, UTI89_C5017 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2J4
#2: Antibody 2H04 Fab light chain


Mass: 23886.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pABVec / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
#3: Antibody 2H04 Fab heavy chain


Mass: 26400.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pABVec / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
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-IDSourceDetails
1Complex of FimCH with 2H04 FabCOMPLEXall0RECOMBINANT
22H04 FabORGANELLE OR CELLULAR COMPONENT#2-#31RECOMBINANT
3FimH adhesin in complex with FimC chaperoneORGANELLE OR CELLULAR COMPONENT#11RECOMBINANTFimH adhesin expressed in complex with FimC chaperone
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Mus musculus (house mouse)10090
43Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Escherichia coli (E. coli)562
32Homo sapiens (human)9606Expi293FABVec
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
250 mMsodium chlorideNaCl1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55.2 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143176 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064647
ELECTRON MICROSCOPYf_angle_d0.8516347
ELECTRON MICROSCOPYf_dihedral_angle_d6.692641
ELECTRON MICROSCOPYf_chiral_restr0.054721
ELECTRON MICROSCOPYf_plane_restr0.007805

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