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- EMDB-48187: Antibody fragments from mAb21 and mAb475 bound to the fimbrial ti... -

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Entry
Database: EMDB / ID: EMD-48187
TitleAntibody fragments from mAb21 and mAb475 bound to the fimbrial tip protein, FimH
Map dataAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Sample
  • Complex: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
    • Complex: Fimbrial tip
      • Protein or peptide: FimH
      • Protein or peptide: FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb475 Heavy Chain Fragment
      • Protein or peptide: mAb475 Light Chain Fragment
      • Protein or peptide: mAb21 Heavy Chain Fragment
      • Protein or peptide: mAb21 Light Chain Fragment
KeywordsFimbrial tip / Lectin domain / Antibody fragments / Antibody-target complex / CELL ADHESION
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 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_48187.png

Downloads & links

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Map

FileDownload / File: emd_48187.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 320 pix.
= 569.6 Å		1.78 Å/pix.
x 320 pix.
= 569.6 Å		1.78 Å/pix.
x 320 pix.
= 569.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.44256762 - 1.1065748
Average (Standard dev.)-0.00046276118 (±0.016919153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 569.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_1.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1 with gaussian filter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_2.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2 with gaussian filter
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 mAb21 and...

Fileemd_48187_additional_3.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
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 mAb21 and...

Fileemd_48187_additional_4.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Antibody fragments from mAb21 and mAb475 bound to...

Fileemd_48187_additional_5.map
AnnotationAntibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 2
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 mAb21 and...

Fileemd_48187_half_map_1.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
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 mAb21 and...

Fileemd_48187_half_map_2.map
AnnotationHalf map of antibody fragments from mAb21 and mAb475 bound to the E. coli adhesin protein FimH, Reconstruction 1
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 mAb21 and mAb475 bound to the fimbrial ti...

EntireName: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
Components
  • Complex: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
    • Complex: Fimbrial tip
      • Protein or peptide: FimH
      • Protein or peptide: FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb475 Heavy Chain Fragment
      • Protein or peptide: mAb475 Light Chain Fragment
      • Protein or peptide: mAb21 Heavy Chain Fragment
      • Protein or peptide: mAb21 Light Chain Fragment

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Supramolecule #1: Antibody fragments from mAb21 and mAb475 bound to the fimbrial ti...

SupramoleculeName: Antibody fragments from mAb21 and mAb475 bound to the fimbrial tip of E. coli
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fimbrial tip

SupramoleculeName: Fimbrial tip / 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

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

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Macromolecule #1: FimH

MacromoleculeName: FimH / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDY PETITDYVTL QRGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR T DKPWPVAL YLTPVSSAGG VAIKAGSLIA VLILRQTNNY NSDDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDY PETITDYVTL QRGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR T DKPWPVAL YLTPVSSAGG VAIKAGSLIA VLILRQTNNY NSDDFQFVWN IYANNDVVVP TG GCDVSAR DVTVTLPDYP GSVPIPLTVY CAKSQNLGYY LSGTTADAGN SIFTNTASFS PAQ GVGVQL TRNGTIIPAN NTVSLGAVGT SAVSLGLTAN YARTGGQVTA GNVQSIIGVT FVYQ

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Macromolecule #2: FimG

MacromoleculeName: FimG / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKWCKRGYVL AAILALASAT IQAADVTITV NGKVVAKPCT VSTTNATVDL GDLYSFSLMS AGAASAWHD VALELTNCPV GTSRVTASFS GAADSTGYYK NQGTAQNIQL ELQDDSGNTL N TGATKTVQ VDDSSQSAHF PLQVRALTVN GGATQGTIQA VISITYTYS

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Macromolecule #3: mAb475 Heavy Chain Fragment

MacromoleculeName: mAb475 Heavy Chain Fragment / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: QVQLQQSGAE LVRPGSSVKI SCKASGYAFS SYWMNWVKQR PGQGLEWIGQ IYPRDGDTNY NGKFMDKVTL TADKSSNTAY MQLSSLTSED SAVYFCEVGR GFYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGSLSSGVHT ...String:
QVQLQQSGAE LVRPGSSVKI SCKASGYAFS SYWMNWVKQR PGQGLEWIGQ IYPRDGDTNY NGKFMDKVTL TADKSSNTAY MQLSSLTSED SAVYFCEVGR GFYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN SGSLSSGVHT FPAVLQSDLY TLSSSVTVPS SPRPSETVTC NVAHPASSTK VDKKI

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Macromolecule #4: mAb475 Light Chain Fragment

MacromoleculeName: mAb475 Light Chain Fragment / type: protein_or_peptide / ID: 4 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: ELQMTQSPKF MSTSVGDRVS VTCKASQNVS NVAWYQQKPG QSPKAMIYSA SYRYSGVPGR FTGSGSGTDF TLTINNVQSE DLATYFCQQN SSFPFTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS ...String:
ELQMTQSPKF MSTSVGDRVS VTCKASQNVS NVAWYQQKPG QSPKAMIYSA SYRYSGVPGR FTGSGSGTDF TLTINNVQSE DLATYFCQQN SSFPFTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TKDEYERHNS YTCEATHKTS TSPIVKSFNR NEC

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Macromolecule #5: mAb21 Heavy Chain Fragment

MacromoleculeName: mAb21 Heavy Chain Fragment / type: protein_or_peptide / ID: 5 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString: EVLLKQSGPE KVKPGASVKI PCKASGYTFT DYNIDWVKQS HGTSLEWIGH LDPNSGGTVY NQKFRGKATL TVDKSSSTAY LELRSLTSED TAVYYCARST MGVYRSDGYY AMDYWGQGTS VTVSSAKTTP PSVYPLAPGC GDTTGSSVTL GCLVKGYFPE SVTVTWNSGS ...String:
EVLLKQSGPE KVKPGASVKI PCKASGYTFT DYNIDWVKQS HGTSLEWIGH LDPNSGGTVY NQKFRGKATL TVDKSSSTAY LELRSLTSED TAVYYCARST MGVYRSDGYY AMDYWGQGTS VTVSSAKTTP PSVYPLAPGC GDTTGSSVTL GCLVKGYFPE SVTVTWNSGS LSSSVHTFPA LLQSGLYTMS SSVTVPSS

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Macromolecule #6: mAb21 Light Chain Fragment

MacromoleculeName: mAb21 Light Chain Fragment / type: protein_or_peptide / ID: 6 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma
SequenceString:
QIVLTQSPAI MSASLGEEIT LTCSASSSIS YMHWYQQKSG TSPKILIYST SNQASGVPSR FSGSGSGTFY SLTISSVEAE DAADYYCHQW SSYPWTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS VVCFLNNFYP KDINVKWKID GSERQNGVLN SWTDQDSKDS TYSMSSTLTL TK

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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
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3222 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 188465
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.4.1)

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