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- EMDB-48393: RB1 Fab bound to 1A6 anti-idiotype Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-48393
TitleRB1 Fab bound to 1A6 anti-idiotype Fab
Map dataEMReady enhanced sharpened map
Sample
  • Complex: RB1 Fab bound to 1A6 anti-idiotype Fab
    • Protein or peptide: 1A6 heavy chain
    • Protein or peptide: 1A6 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: 3.67 Å
AuthorsWarren C
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Vaccines (Basel) / Year: 2025
Title: Anti-Idiotypic Antibody as a Booster Vaccine Against Respiratory Syncytial Virus
Authors: Mukhopadhyay S / Manolaridis I / Warren C / Tang A / O'Donnell G / Luo B / Staupe RP / Vora KA / Chen Z
History
DepositionDec 20, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48393.png

Downloads & links

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Map

FileDownload / File: emd_48393.map.gz / Format: CCP4 / Size: 40.7 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 340 pix.
= 170. Å		0.5 Å/pix.
x 190 pix.
= 95. Å		0.5 Å/pix.
x 165 pix.
= 82.5 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-0.16531533 - 14.795968
Average (Standard dev.)0.25263155 (±1.3328516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin214231143
Dimensions190165340
Spacing165190340
CellA: 82.5 Å / B: 95.0 Å / C: 170.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_48393_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_48393_additional_2.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfA

Fileemd_48393_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_48393_half_map_2.map
AnnotationhalfB
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 1A6 anti-idiotype Fab

EntireName: RB1 Fab bound to 1A6 anti-idiotype Fab
Components
  • Complex: RB1 Fab bound to 1A6 anti-idiotype Fab
    • Protein or peptide: 1A6 heavy chain
    • Protein or peptide: 1A6 light chain
    • Protein or peptide: RB1 heavy chain
    • Protein or peptide: RB1 light chain

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Supramolecule #1: RB1 Fab bound to 1A6 anti-idiotype Fab

SupramoleculeName: RB1 Fab bound to 1A6 anti-idiotype Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1A6 heavy chain

MacromoleculeName: 1A6 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.557316 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMNWVRQA PGKGLEWVSL ISGSGSSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARF HTHGGYFDIW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
QVQLVESGGG LVQPGGSLRL SCAASGFTFS SYAMNWVRQA PGKGLEWVSL ISGSGSSTYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARF HTHGGYFDIW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCD

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Macromolecule #2: 1A6 light chain

MacromoleculeName: 1A6 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.735072 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIALTQPASV SGSPGQSITI SCTGTSSDIG AYTYGSWYQQ HPGKAPKLMI YGVNNRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CASFDFSVSG VVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
DIALTQPASV SGSPGQSITI SCTGTSSDIG AYTYGSWYQQ HPGKAPKLMI YGVNNRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CASFDFSVSG VVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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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) / Number real images: 11590 / 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: 2.2 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: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 689729
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9mml:
RB1 Fab bound to 1A6 anti-idiotype Fab

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