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- EMDB-26528: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-26528
TitleSARS-CoV-2 6P Mut7 in complex with K398.8 Fab
Map data
Sample
  • Complex: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2
      • Complex: K398.8 Fab
KeywordsSARS-CoV-1 / SARS-CoV-2 / sarbecoronaviruses / cross-reactive antibody / RBD / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLee WH / Torres JL / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Sci Transl Med / Year: 2022
Title: Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.
Authors: Wan-Ting He / Meng Yuan / Sean Callaghan / Rami Musharrafieh / Ge Song / Murillo Silva / Nathan Beutler / Wen-Hsin Lee / Peter Yong / Jonathan L Torres / Mariane Melo / Panpan Zhou / Fangzhu ...Authors: Wan-Ting He / Meng Yuan / Sean Callaghan / Rami Musharrafieh / Ge Song / Murillo Silva / Nathan Beutler / Wen-Hsin Lee / Peter Yong / Jonathan L Torres / Mariane Melo / Panpan Zhou / Fangzhu Zhao / Xueyong Zhu / Linghang Peng / Deli Huang / Fabio Anzanello / James Ricketts / Mara Parren / Elijah Garcia / Melissa Ferguson / William Rinaldi / Stephen A Rawlings / David Nemazee / Davey M Smith / Bryan Briney / Yana Safonova / Thomas F Rogers / Jennifer M Dan / Zeli Zhang / Daniela Weiskopf / Alessandro Sette / Shane Crotty / Darrell J Irvine / Andrew B Ward / Ian A Wilson / Dennis R Burton / Raiees Andrabi /
Abstract: To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting broadly neutralizing antibody responses to CoVs. Here, we show that immunization of ...To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting broadly neutralizing antibody responses to CoVs. Here, we show that immunization of macaques with SARS-CoV-2 spike (S) protein with a two-shot protocol generated potent serum receptor binding domain cross-neutralizing antibody responses to both SARS-CoV-2 and SARS-CoV-1. Furthermore, responses were equally effective against most SARS-CoV-2 variants of concern (VOCs) and some were highly effective against Omicron. This result contrasts with human infection or many two-shot vaccination protocols where responses were typically more SARS-CoV-2 specific and where VOCs were less well neutralized. Structural studies showed that cloned macaque neutralizing antibodies, particularly using a given heavy chain germline gene, recognized a relatively conserved region proximal to the angiotensin converting enzyme 2 receptor binding site (RBS), whereas many frequently elicited human neutralizing antibodies targeted more variable epitopes overlapping the RBS. B cell repertoire differences between humans and macaques appeared to influence the vaccine response. The macaque neutralizing antibodies identified a pan-SARS-related virus epitope region less well targeted by human antibodies that could be exploited in rational vaccine design.
History
DepositionMar 28, 2022-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26528.png

Downloads & links

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Map

FileDownload / File: emd_26528.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0107
Minimum - Maximum-0.05070299 - 0.10119588
Average (Standard dev.)-0.000020093365 (±0.0039301803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26528_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_26528_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 : SARS-CoV-2 6P Mut7 in complex with K398.8 Fab

EntireName: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab
Components
  • Complex: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2
      • Complex: K398.8 Fab

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Supramolecule #1: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab

SupramoleculeName: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab / type: complex / ID: 1 / Parent: 0 / Details: SARS-CoV-2 6P Mut7

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: complex / ID: 2 / Parent: 1 / Details: SARS-CoV-2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: K398.8 Fab

SupramoleculeName: K398.8 Fab / type: complex / ID: 3 / Parent: 2 / Details: K398.8 Fab
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vyb

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 19786
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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