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- EMDB-48404: RB1 Fab bound to 1D4 anti-idiotype Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-48404
TitleRB1 Fab bound to 1D4 anti-idiotype Fab
Map dataEMReady enhanced sharpened map
Sample
  • Complex: RB1 Fab bound to 1D4 anti-idiotype Fab
    • Protein or peptide: 1D4 heavy chain
    • Protein or peptide: 1D4 light chain
    • Protein or peptide: RB1 heavy chain
    • Protein or peptide: RB1 light chain
KeywordsFab anti idiotype RSV / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsWarren C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Vaccines (Basel) / Year: 2025
Title: Anti-Idiotypic Antibody as a Booster Vaccine Against Respiratory Syncytial Virus.
Authors: Shreya Mukhopadhyay / Ioannis Manolaridis / Christopher Warren / Aimin Tang / Gregory O'Donnell / Bin Luo / Ryan P Staupe / Kalpit A Vora / Zhifeng Chen /
Abstract: The respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in children and adults. With nearly everyone infected by the age of five, there is an opportunity to ... The respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in children and adults. With nearly everyone infected by the age of five, there is an opportunity to develop booster vaccines that enhance B-cell immunity, promoting potent and broadly neutralizing antibodies. One potential approach involves using anti-idiotypic antibodies (anti-IDs) to mimic specific antigenic sites and enhance preexisting immunity in an epitope-specific manner. RB1, a monoclonal antibody (mAb) that binds to site IV of the RSV fusion (RSV F) protein, is a potent and broadly neutralizing against RSV A and B viruses. It is the precursor for MK1654 (clesrovimab), which successfully completed a Phase III clinical trial. In this study, we isolated two anti-IDs, 1A6 and 1D4, targeting RB1 CDR regions, demonstrating that 1A6 competes fully with RSV F in binding to RB1. We resolved the RB1-1A6 and RB1-1D4 Fab-Fab complex structures and proved that 1A6 mimics the RSV F site IV better than 1D4. In an immunogenicity study, mice primed with RSV F and boosted with 1A6 Fab showed a site IV-specific antibody response with a concurrent increase in RSV virus neutralization. These results suggest that anti-IDs could be potentially used as booster vaccines for specific epitopes.
History
DepositionDec 20, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48404.png

Downloads & links

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Map

FileDownload / File: emd_48404.map.gz / Format: CCP4 / Size: 25.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMReady enhanced sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 307 pix.
= 153.5 Å		0.5 Å/pix.
x 165 pix.
= 82.5 Å		0.5 Å/pix.
x 134 pix.
= 67. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-0.16437721 - 15.599214
Average (Standard dev.)0.369146 (±1.521052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions165134307
Spacing134165307
CellA: 67.0 Å / B: 82.5 Å / C: 153.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map

Fileemd_48404_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_48404_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_48404_half_map_1.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_48404_half_map_2.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RB1 Fab bound to 1D4 anti-idiotype Fab

EntireName: RB1 Fab bound to 1D4 anti-idiotype Fab
Components
  • Complex: RB1 Fab bound to 1D4 anti-idiotype Fab
    • Protein or peptide: 1D4 heavy chain
    • Protein or peptide: 1D4 light chain
    • Protein or peptide: RB1 heavy chain
    • Protein or peptide: RB1 light chain

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Supramolecule #1: RB1 Fab bound to 1D4 anti-idiotype Fab

SupramoleculeName: RB1 Fab bound to 1D4 anti-idiotype Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1D4 heavy chain

MacromoleculeName: 1D4 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.029652 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVESGGG LVQPGGSLRL SCAASGFTFS SSGLHWVRQA PGKGLEWVSG IDSSSSTTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARY YFDVWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP ...String:
QVQLVESGGG LVQPGGSLRL SCAASGFTFS SSGLHWVRQA PGKGLEWVSG IDSSSSTTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARY YFDVWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA L TSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD

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Macromolecule #2: 1D4 light chain

MacromoleculeName: 1D4 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.444598 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIELTQPPSV SVAPGQTARI SCSGDSIGTY AYWYQQKPGQ APVLVIYADD NRPSGIPERF SGSNSGNTAT LTISGTQAED EADYYCSSW ATDNAPVFGG GTKLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS ...String:
DIELTQPPSV SVAPGQTARI SCSGDSIGTY AYWYQQKPGQ APVLVIYADD NRPSGIPERF SGSNSGNTAT LTISGTQAED EADYYCSSW ATDNAPVFGG GTKLTVLGQP KAAPSVTLFP PSSEELQANK ATLVCLISDF YPGAVTVAWK ADSSPVKAGV E TTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TECS

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Macromolecule #3: RB1 heavy chain

MacromoleculeName: RB1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.551439 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGG LVRPGRSLRL SCTVSGFSFD DSAMSWVRQA PGKGLEWISF IKSKTYGGTK EYAASVKGRF TISRDDSKNI AYLQMNSLK TEDTAVYYCT RGAPYGGNSD YYYGLDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LVRPGRSLRL SCTVSGFSFD DSAMSWVRQA PGKGLEWISF IKSKTYGGTK EYAASVKGRF TISRDDSKNI AYLQMNSLK TEDTAVYYCT RGAPYGGNSD YYYGLDVWGQ GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #4: RB1 light chain

MacromoleculeName: RB1 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.406043 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRTSQDVR GALAWYQQKP GKAPKLLIFD ASSLETGVPS RFSGSGSGTV FTLTISSLQP EDFAAYYCQ QFLDFPFTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRTSQDVR GALAWYQQKP GKAPKLLIFD ASSLETGVPS RFSGSGSGTV FTLTISSLQP EDFAAYYCQ QFLDFPFTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240676
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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