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- PDB-9ptm: Antibody fragment from mAb824 bound to the adhesin protein FimH. -

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Basic information

Entry
Database: PDB / ID: 9ptm
TitleAntibody fragment from mAb824 bound to the adhesin protein FimH.
Components
  • Protein FimG
  • Type 1 fimbrin D-mannose specific adhesin
  • mAb824 Heavy Chain
  • mAb824 Light Chain
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: 3.4 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: To Be Published
Title: Antibodies disrupt bacterial adhesion by ligand mimicry and allostery
Authors: Hvorecny, K.L. / Kollman, J.M.
History
DepositionJul 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,1014
Polymers93,1014
Non-polymers00
Water00
1


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

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Components

#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
#3: Antibody mAb824 Heavy Chain


Mass: 22526.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody mAb824 Light Chain


Mass: 21757.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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 fragment from mAb824 bound to the E. coli adhesin protein FimHCOMPLEXall0MULTIPLE SOURCES
2Fimbrial tipCOMPLEX#1-#21RECOMBINANT
3Antibody FragmentsCOMPLEX#3-#41NATURAL
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 hybridoma
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
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 recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10383

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
2SerialEM4.1image acquisition
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.9model fitting
8ISOLDE1.6model fitting
10PHENIX1.21.1_5286model refinement
11cryoSPARC4.5.3initial Euler assignment
12RELION5final Euler assignment
14PHENIX1.21.1-52863D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 306269 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 9ME5

9me5


Accession code: 9ME5 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046346
ELECTRON MICROSCOPYf_angle_d0.598683
ELECTRON MICROSCOPYf_dihedral_angle_d6.342892
ELECTRON MICROSCOPYf_chiral_restr0.0451011
ELECTRON MICROSCOPYf_plane_restr0.0051120

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