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- PDB-9me4: Antibody fragments from mAb475 and mAb824 bound to the adhesin pr... -

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Basic information

Entry
Database: PDB / ID: 9me4
TitleAntibody fragments from mAb475 and mAb824 bound to the adhesin protein FimH
Components
  • Protein FimG
  • Type 1 fimbrin D-mannose specific adhesin
  • mAb475 Heavy Chain Fragment
  • mAb475 Light Chain Fragment
  • mAb824 Heavy Chain Fragment
  • mAb824 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)
Escherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
DepositionDec 6, 2024Deposition 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
H: mAb475 Heavy Chain Fragment
I: mAb824 Heavy Chain Fragment
L: mAb475 Light Chain Fragment
M: mAb824 Light Chain Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,6157
Polymers139,7046
Non-polymers9111
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, mass spectrometry, 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 K-12 (bacteria) / Strain: K-12 / 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 mAb475 Heavy Chain Fragment


Mass: 23105.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: 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) / Tissue: B cell hybridoma
#5: Antibody mAb475 Light Chain Fragment


Mass: 23496.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: 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) / Tissue: B cell hybridoma

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Sugars , 1 types, 1 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestY
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 mAb475 and mAb824 bound to the E. coli adhesin protein FimHCOMPLEX#1-#4, #60MULTIPLE SOURCES
2Fimbrial tipCOMPLEX#1-#21RECOMBINANT
3Antibody FragmentsCOMPLEX#3-#4, #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 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 mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationCryogen 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: 7832

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.4.1particle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARCv4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129751 / 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
RefinementHighest resolution: 3.2 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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