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- EMDB-47153: Single particle cryoelectron microscopy of respiratory syncytial ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47153
TitleSingle particle cryoelectron microscopy of respiratory syncytial virus G ectodomain in complex with Fabs 2D10 and 3D3
Map data
Sample
  • Complex: Respiratory syncytial virus G ectodomain in complex with Fabs 2D10 and 3D3
    • Protein or peptide: Respiratory syncytial virus G ectodomain (RSVG)
    • Protein or peptide: mAb 2D10 Fab Heavy chain
    • Protein or peptide: mAb 3D3 Fab heavy chain
    • Protein or peptide: mAb 3D3 light chain
    • Protein or peptide: mAb 2D10 Light chain
Keywordsrespiratory syncytial virus G ectodomain / Fab 2D10 / Fab 3D3 / VIRAL PROTEIN
Biological speciesRespiratory syncytial virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.29 Å
AuthorsO'Rourke S / Juarez MG / Balasco Serrao VH / DuBois RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI166066 United States
CitationJournal: Sci Rep / Year: 2025
Title: Structures of respiratory syncytial virus G bound to broadly reactive antibodies provide insights into vaccine design.
Authors: Maria G Juarez / Sara M O'Rourke / John V Dzimianski / Delia Gagnon / Gabriel Penunuri / Vitor H B Serrão / Russell B Corbett-Detig / Lawrence M Kauvar / Rebecca M DuBois /
Abstract: Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 ...Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 to promote viral entry and modulate host immunity. Antibodies against RSV G are a known correlate of protection. Previously, several broadly reactive, high-affinity anti-RSV G human monoclonal antibodies were isolated from RSV-exposed individuals and were shown to be protective in vitro and in vivo. Here, we determined the structures of three of these antibodies in complex with RSV G and defined distinct conformational epitopes comprised of highly conserved RSV G residues. Binding competition and structural studies demonstrated that this highly conserved region displays two non-overlapping antigenic sites. Analyses of anti-RSV G antibody sequences reveal that antigenic site flexibility may promote the elicitation of diverse antibody germlines. Together, these findings provide a foundation for next-generation RSV prophylactics, and they expand concepts in vaccine design for the elicitation of germline lineage-diverse, broadly reactive, high-affinity antibodies.
History
DepositionSep 30, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47153.png

Downloads & links

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Map

FileDownload / File: emd_47153.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 320 pix.
= 221.28 Å		0.69 Å/pix.
x 320 pix.
= 221.28 Å		0.69 Å/pix.
x 320 pix.
= 221.28 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6915 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0186
Minimum - Maximum0.0 - 0.20801057
Average (Standard dev.)0.0009874784 (±0.008020246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 221.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47153_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47153_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Respiratory syncytial virus G ectodomain in complex with Fabs 2D1...

EntireName: Respiratory syncytial virus G ectodomain in complex with Fabs 2D10 and 3D3
Components
  • Complex: Respiratory syncytial virus G ectodomain in complex with Fabs 2D10 and 3D3
    • Protein or peptide: Respiratory syncytial virus G ectodomain (RSVG)
    • Protein or peptide: mAb 2D10 Fab Heavy chain
    • Protein or peptide: mAb 3D3 Fab heavy chain
    • Protein or peptide: mAb 3D3 light chain
    • Protein or peptide: mAb 2D10 Light chain

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Supramolecule #1: Respiratory syncytial virus G ectodomain in complex with Fabs 2D1...

SupramoleculeName: Respiratory syncytial virus G ectodomain in complex with Fabs 2D10 and 3D3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus

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Macromolecule #1: Respiratory syncytial virus G ectodomain (RSVG)

MacromoleculeName: Respiratory syncytial virus G ectodomain (RSVG) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: SVLASEFSAN HKVTPTTAII QDATSQIKNT TPTYLTQNPQ LGISPSNPSE ITSQITTILA STTPGVKSTL QSTTVKTKNT TTTQTQPSKP TTKQRQNKPP SKPNNDFHFE VFNFVPCSIC SNNPTCWAIC KRIPNKKPGK KTTTKPTKKP TLKTTKKDPK PQTTKSKEVP ...String:
SVLASEFSAN HKVTPTTAII QDATSQIKNT TPTYLTQNPQ LGISPSNPSE ITSQITTILA STTPGVKSTL QSTTVKTKNT TTTQTQPSKP TTKQRQNKPP SKPNNDFHFE VFNFVPCSIC SNNPTCWAIC KRIPNKKPGK KTTTKPTKKP TLKTTKKDPK PQTTKSKEVP TTKPTEEPTI NTTKTNIITT LLTSNTTGNP ELTSQMETFH STSSEGNPSP SQVSTTSEYP SQPSSPPNTP RQHHHHHHGW SHPQFEKGGG SGGGSGGGSW SHPQFEK

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Macromolecule #2: mAb 2D10 Fab Heavy chain

MacromoleculeName: mAb 2D10 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGPE VKKPGASVRL SCKASGYVFT NYGVSWVRQA PGQGLEWMGW SSPYNGNTYY AQKLKARVTM TTDTSTNTAY MELRSLRSDD TAVYYCGRDM LGVVQAVAGP FDSWGQGTLV TVSSASASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG ...String:
QVQLVQSGPE VKKPGASVRL SCKASGYVFT NYGVSWVRQA PGQGLEWMGW SSPYNGNTYY AQKLKARVTM TTDTSTNTAY MELRSLRSDD TAVYYCGRDM LGVVQAVAGP FDSWGQGTLV TVSSASASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KTH

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Macromolecule #3: mAb 3D3 Fab heavy chain

MacromoleculeName: mAb 3D3 Fab heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EEQLVESGGG LVQPGRSLRL SCVGSGLRFE EHAMHWVRQA PGRGLEWVSG ISWNSGSVGY ADSVKGRFTT SRDNAKDILF LEMNTLRSED TALYFCAIMV ATTKNDFHYY KDVWGKGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL ...String:
EEQLVESGGG LVQPGRSLRL SCVGSGLRFE EHAMHWVRQA PGRGLEWVSG ISWNSGSVGY ADSVKGRFTT SRDNAKDILF LEMNTLRSED TALYFCAIMV ATTKNDFHYY KDVWGKGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT H

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Macromolecule #4: mAb 3D3 light chain

MacromoleculeName: mAb 3D3 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QIVLTQSPAT LSLSPGERAT LSCRASQSVS NHLAWYQQKP GQAPRLLIYE TSNRATGIPP RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RNNWYTFGQG TKLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE SVTEQDSKDS ...String:
QIVLTQSPAT LSLSPGERAT LSCRASQSVS NHLAWYQQKP GQAPRLLIYE TSNRATGIPP RFSGSGSGTD FTLTISSLEP EDFAVYYCQQ RNNWYTFGQG TKLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #5: mAb 2D10 Light chain

MacromoleculeName: mAb 2D10 Light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DTPMTQSPSS VSASVGDRVT ISCRASQGIS NSLAWYQQKL GKAPQLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQQ TNTFPFTFGP GTKVEVRRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK ...String:
DTPMTQSPSS VSASVGDRVT ISCRASQGIS NSLAWYQQKL GKAPQLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQQ TNTFPFTFGP GTKVEVRRRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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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: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 481593
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 50831
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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