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- EMDB-60274: SARS-CoV-2 XBB.1.5 spike glycoprotein trimer in complex with anti... -

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Basic information

Entry
Database: EMDB / ID: EMD-60274
TitleSARS-CoV-2 XBB.1.5 spike glycoprotein trimer in complex with antigen-binding fragments (Fabs)
Map datab-factor sharpened map
Sample
  • Complex: SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex
    • Complex: Antigen-binding fragments (Fab)
    • Complex: SARS-CoV-2 XBB.1.5 spike glyco protein
KeywordsComplex / VIRAL PROTEIN
Biological speciesSARS-CoV-2 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsSugita Y / Kimura K / Noda T / Hashiguchi T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21ym0126048 Japan
CitationJournal: EBioMedicine / Year: 2024
Title: Induction of IGHV3-53 public antibodies with broadly neutralising activity against SARS-CoV-2 including Omicron subvariants in a Delta breakthrough infection case.
Authors: Takeo Kuwata / Yu Kaku / Shashwata Biswas / Kaho Matsumoto / Mikiko Shimizu / Yoko Kawanami / Ryuta Uraki / Kyo Okazaki / Rumi Minami / Yoji Nagasaki / Mami Nagashima / Isao Yoshida / Kenji ...Authors: Takeo Kuwata / Yu Kaku / Shashwata Biswas / Kaho Matsumoto / Mikiko Shimizu / Yoko Kawanami / Ryuta Uraki / Kyo Okazaki / Rumi Minami / Yoji Nagasaki / Mami Nagashima / Isao Yoshida / Kenji Sadamasu / Kazuhisa Yoshimura / Mutsumi Ito / Maki Kiso / Seiya Yamayoshi / Masaki Imai / Terumasa Ikeda / Kei Sato / Mako Toyoda / Takamasa Ueno / Takako Inoue / Yasuhito Tanaka / Kanako Tarakado Kimura / Takao Hashiguchi / Yukihiko Sugita / Takeshi Noda / Hiroshi Morioka / Yoshihiro Kawaoka / Shuzo Matsushita / /
Abstract: BACKGROUND: Emergence of SARS-CoV-2 variants that escape neutralising antibodies hampers the development of vaccines and therapeutic antibodies against SARS-CoV-2. IGHV3-53/3-66-derived public ...BACKGROUND: Emergence of SARS-CoV-2 variants that escape neutralising antibodies hampers the development of vaccines and therapeutic antibodies against SARS-CoV-2. IGHV3-53/3-66-derived public antibodies, which are generally specific to the prototype virus and are frequently induced in infected or vaccinated individuals, show minimal affinity maturation and high potency against prototype SARS-CoV-2.
METHODS: Monoclonal antibodies isolated from a Delta breakthrough infection case were analysed for cross-neutralising activities against SARS-CoV-2 variants. The broadly neutralising antibody K4-66 ...METHODS: Monoclonal antibodies isolated from a Delta breakthrough infection case were analysed for cross-neutralising activities against SARS-CoV-2 variants. The broadly neutralising antibody K4-66 was further analysed in a hamster model, and the effect of somatic hypermutations was assessed using the inferred germline precursor.
FINDINGS: Antibodies derived from IGHV3-53/3-66 showed broader neutralising activity than antibodies derived from IGHV1-69 and other IGHV genes. IGHV3-53/3-66 antibodies neutralised the Delta variant ...FINDINGS: Antibodies derived from IGHV3-53/3-66 showed broader neutralising activity than antibodies derived from IGHV1-69 and other IGHV genes. IGHV3-53/3-66 antibodies neutralised the Delta variant better than the IGHV1-69 antibodies, suggesting that the IGHV3-53/3-66 antibodies were further maturated by Delta breakthrough infection. One IGHV3-53/3-66 antibody, K4-66, neutralised all Omicron subvariants tested, including EG.5.1, BA.2.86, and JN.1, and decreased the viral load in the lungs of hamsters infected with Omicron subvariant XBB.1.5. The importance of somatic hypermutations was demonstrated by the loss of neutralising activity of the inferred germline precursor of K4-66 against Beta and Omicron variants.
INTERPRETATION: Broadly neutralising IGHV3-53/3-66 antibodies have potential as a target for the development of effective vaccines and therapeutic antibodies against newly emerging SARS-CoV-2 variants.
FUNDING: This work was supported by grants from AMED (JP23ym0126048, JP22ym0126048, JP21ym0126048, JP23wm0125002, JP233fa627001, JP223fa627009, JP24jf0126002, and JP22fk0108572), and the JSPS ...FUNDING: This work was supported by grants from AMED (JP23ym0126048, JP22ym0126048, JP21ym0126048, JP23wm0125002, JP233fa627001, JP223fa627009, JP24jf0126002, and JP22fk0108572), and the JSPS (JP21H02970, JK23K20041, and JPJSCCA20240006).
History
DepositionMay 27, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60274.png

Downloads & links

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Map

FileDownload / File: emd_60274.map.gz / Format: CCP4 / Size: 152.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationb-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 342 pix.
= 316.35 Å		0.93 Å/pix.
x 342 pix.
= 316.35 Å		0.93 Å/pix.
x 342 pix.
= 316.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.925 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.43544054 - 0.79701513
Average (Standard dev.)-0.00040951677 (±0.022052795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions342342342
Spacing342342342
CellA=B=C: 316.35 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60274_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: a locally refined map

Fileemd_60274_additional_1.map
Annotationa locally refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: a half map

Fileemd_60274_half_map_1.map
Annotationa half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: a half map

Fileemd_60274_half_map_2.map
Annotationa half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex

EntireName: SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex
Components
  • Complex: SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex
    • Complex: Antigen-binding fragments (Fab)
    • Complex: SARS-CoV-2 XBB.1.5 spike glyco protein

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Supramolecule #1: SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex

SupramoleculeName: SARS-CoV-2 XBB.1.5 spike glyco protein-human Fab complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: SARS-CoV-2 (virus) / Strain: XBB.1.5

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Supramolecule #2: Antigen-binding fragments (Fab)

SupramoleculeName: Antigen-binding fragments (Fab) / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: SARS-CoV-2 XBB.1.5 spike glyco protein

SupramoleculeName: SARS-CoV-2 XBB.1.5 spike glyco protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: SARS-CoV-2 (virus) / Strain: XBB.1.5

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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: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: 10 mA
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: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5469 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1222638
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1.1) / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 60704
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 4.1.1)
FSC plot (resolution estimation)

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