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- EMDB-48184: Antibody fragments from mAb824 and mAb926 bound to the adhesin pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-48184
TitleAntibody fragments from mAb824 and mAb926 bound to the adhesin protein FimH
Map dataAntibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
Sample
  • Complex: Antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
    • Complex: Fimbrial tip (FimH and FimG)
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
      • Protein or peptide: Protein FimG
    • Complex: Antibody Fragments, Heavy and Light Chains
      • Protein or peptide: mAb926 Heavy Chain Fragment
      • Protein or peptide: mAb824 Heavy Chain Fragment
      • Protein or peptide: mAb926 Light Chain Fragment
      • Protein or peptide: mAb824 Light Chain Fragment
KeywordsFimbrial 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHvorecny KL / Magala P / Klevit RE / Kollman JM
Funding support United States, 4 items
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 KL / Kollman JM
History
DepositionDec 6, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48184.png

Downloads & links

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Map

FileDownload / File: emd_48184.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.12 Å/pix.
x 480 pix.
= 539.52 Å		1.12 Å/pix.
x 480 pix.
= 539.52 Å		1.12 Å/pix.
x 480 pix.
= 539.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-22.701840000000001 - 28.964480999999999
Average (Standard dev.)-0.0000011980064 (±0.17426053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 539.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Antibody fragments from mAb824 and mAb926 bound to...

Fileemd_48184_additional_1.map
AnnotationAntibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map of antibody fragments from mAb824 and...

Fileemd_48184_additional_2.map
AnnotationHalf map of antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map of antibody fragments from mAb824 and...

Fileemd_48184_additional_3.map
AnnotationHalf map of antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of antibody fragments from mAb824 and...

Fileemd_48184_half_map_1.map
AnnotationHalf map of antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of antibody fragments from mAb824 and...

Fileemd_48184_half_map_2.map
AnnotationHalf map of antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody fragments from mAb824 and mAb926 bound to the E. coli ad...

EntireName: Antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
Components
  • Complex: Antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
    • Complex: Fimbrial tip (FimH and FimG)
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
      • Protein or peptide: Protein FimG
    • Complex: Antibody Fragments, Heavy and Light Chains
      • Protein or peptide: mAb926 Heavy Chain Fragment
      • Protein or peptide: mAb824 Heavy Chain Fragment
      • Protein or peptide: mAb926 Light Chain Fragment
      • Protein or peptide: mAb824 Light Chain Fragment

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Supramolecule #1: Antibody fragments from mAb824 and mAb926 bound to the E. coli ad...

SupramoleculeName: Antibody fragments from mAb824 and mAb926 bound to the E. coli adhesin protein FimH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fimbrial tip (FimH and FimG)

SupramoleculeName: Fimbrial tip (FimH and FimG) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Antibody Fragments, Heavy and Light Chains

SupramoleculeName: Antibody Fragments, Heavy and Light Chains / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell

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Macromolecule #1: Type 1 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.48826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN IYANNDVVVP TGGCDVSARD VTVTLPDYPG SVPIPLTVYC AKSQNLGYYL SGTTADAGNS IFTNTASFSP AQ GVGVQLT RNGTIIPANN TVSLGAVGTS AVSLGLTANY ARTGGQVTAG NVQSIIGVTF VYQ

UniProtKB: Type 1 fimbrin D-mannose specific adhesin

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Macromolecule #2: Protein FimG

MacromoleculeName: Protein FimG / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.328258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKWCKRGYVL AAILALASAT IQAADVTITV NGKVVAKPCT VSTTNATVDL GDLYSFSLMS AGAASAWHDV ALELTNCPVG TSRVTASFS GAADSTGYYK NQGTAQNIQL ELQDDSGNTL NTGATKTVQV DDSSQSAHFP LQVRALTVNG GATQGTIQAV I SITYTYS

UniProtKB: Protein FimG

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Macromolecule #3: mAb926 Heavy Chain Fragment

MacromoleculeName: mAb926 Heavy Chain Fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.703312 KDa
SequenceString: QVQLQQSGAE LATPGASVKM SCKASGYTST NYWIHWVKQR PGQGLEWIGY INPTSGYTEY NQNFKDKATL TADKSSSTAY MQLTSLTSE DSAVYYCARG VIRDFWGQGT TLTVSSAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP EPVTVTWNSG S LSSGVHTF ...String:
QVQLQQSGAE LATPGASVKM SCKASGYTST NYWIHWVKQR PGQGLEWIGY INPTSGYTEY NQNFKDKATL TADKSSSTAY MQLTSLTSE DSAVYYCARG VIRDFWGQGT TLTVSSAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP EPVTVTWNSG S LSSGVHTF PAVLQSDLYT LSSSVTVPSS PRPSETVTCN VAHPASSTKV DKKI

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Macromolecule #4: mAb824 Heavy Chain Fragment

MacromoleculeName: mAb824 Heavy Chain Fragment / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.526971 KDa
SequenceString: EIQLQQSGPE RMKPGASVKI SCKASGYSFT TYYIHWVKQS HGRSLEWIGY IDPFNDDTNY NQKFKGKATL TVDKSSSTAY MHLSSLTSE DSAVYYCARS YYGSLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH ...String:
EIQLQQSGPE RMKPGASVKI SCKASGYSFT TYYIHWVKQS HGRSLEWIGY IDPFNDDTNY NQKFKGKATL TVDKSSSTAY MHLSSLTSE DSAVYYCARS YYGSLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSETVT CNVAHPASST

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Macromolecule #5: mAb926 Light Chain Fragment

MacromoleculeName: mAb926 Light Chain Fragment / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.222803 KDa
SequenceString: ELVMTQTPLS LPVSLGDQAS ISCRSSQNIV HNNGNTYLEW YLQSPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PFTFGSGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
ELVMTQTPLS LPVSLGDQAS ISCRSSQNIV HNNGNTYLEW YLQSPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGSHV PFTFGSGTKL EIKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRNE C

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Macromolecule #6: mAb824 Light Chain Fragment

MacromoleculeName: mAb824 Light Chain Fragment / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.757852 KDa
SequenceString: DIQMTQTTSS LSASLGDRVT ISCRASQGVN NYLNWYQQKP DGSVKLLIYY TSNLHSGAPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QANMVPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCRASQGVN NYLNWYQQKP DGSVKLLIYY TSNLHSGAPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QANMVPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEAR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 15349 / #0 - Average electron dose: 42.0 e/Å2 / #0 - Details: SerialEM / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 1651 / #1 - Average electron dose: 55.0 e/Å2 / #1 - Details: Leginon
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253258
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5

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Atomic model buiding 1

Initial model
PDB IDChain

3jwn

source_name: PDB, initial_model_type: experimental model

15c8

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9me5:
Antibody fragments from mAb824 and mAb926 bound to the adhesin protein FimH

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