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Research Article
Structural characterisation of a nanobody derived from a naïve library that neutralises SARS-CoV-2
Raymond J. Owens
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK
Corresponding Author
James H. Naismith
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK
Corresponding Author
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This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Nature Portfolio.
The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than seasonal flu. The SARS-CoV-2 receptor binding domain (RBD) of the Spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naïve llama single chain nanobody library and PCR maturation we have produced a nanobody, H11-D4, with a KD 9 nM for RBD that blocks the binding of RBD to the ACE2. Single particle cryo-electron microscopy revealed that H11-D4 binds to each of the three RBDs in the Spike trimer. The 1.8 Å crystal structure of the H11-D4 – RBD complex has illuminated the molecular interactions that drive the high affinity. H11-D4 binds to an epitope on RBD that overlaps with the ACE2 binding, explaining the blocking of ACE2 binding. The nanobody showed potent neutralising activity against live SARS-CoV-2 virus.
Keywords
SARS-CoV-2, nanobody, H11-D4, spike protein receptor binding domain, human angiotensin-converting enzyme 2
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James H. Naismith
ORCiDcommented on 01 June, 2020
Although, the authors are convinced of the significance and quality of the manuscript. I would emphasise that this is a preprint and should not be relied on until it has been peer reviewed. The authors are trying to avoid all commentary on the work until it has been peer reviewed.
James H. Naismith
ORCiDcommented on 30 June, 2020
As an update, we received two reviews. Both requested additional data and analysis. This is what peer review is for, to help make better papers. We have carried out these experiments and resubmitted the paper. . I do not think science by press release is suitable for the vast bulk of basic biomedical science and we have avoided and will continue to avoid any comments if and until an accepted paper appears.
James H. Naismith
ORCiDcommented on 03 July, 2020
The revised paper has ended its journey through the peer review system. The now accepted revision is embargoed pending publication. We will distribute reagents in the paper to researchers of course, the coordinates are accessible at the RCSB and the gene products being deposited with Addgene.
View 1 reply
James H. Naismith
ORCiDcommented on 13 July, 2020
The final version now online. https://www.nature.com/articles/s41594-020-0469-6
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Research Article
Structural characterisation of a nanobody derived from a naïve library that neutralises SARS-CoV-2
Raymond J. Owens
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK
Corresponding Author
James H. Naismith
Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0FA, UK
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Metrics
Comments: 5
PDF Downloads: ...
HTML Views: ...
Subject Areas
Molecular Biology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at Nature Portfolio.
The SARS-CoV-2 virus is more transmissible than previous coronaviruses and causes a more serious illness than seasonal flu. The SARS-CoV-2 receptor binding domain (RBD) of the Spike protein binds to the human angiotensin-converting enzyme 2 (ACE2) receptor as a prelude to viral entry into the cell. Using a naïve llama single chain nanobody library and PCR maturation we have produced a nanobody, H11-D4, with a KD 9 nM for RBD that blocks the binding of RBD to the ACE2. Single particle cryo-electron microscopy revealed that H11-D4 binds to each of the three RBDs in the Spike trimer. The 1.8 Å crystal structure of the H11-D4 – RBD complex has illuminated the molecular interactions that drive the high affinity. H11-D4 binds to an epitope on RBD that overlaps with the ACE2 binding, explaining the blocking of ACE2 binding. The nanobody showed potent neutralising activity against live SARS-CoV-2 virus.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
James H. Naismith
ORCiDcommented on 01 June, 2020
Although, the authors are convinced of the significance and quality of the manuscript. I would emphasise that this is a preprint and should not be relied on until it has been peer reviewed. The authors are trying to avoid all commentary on the work until it has been peer reviewed.
James H. Naismith
ORCiDcommented on 30 June, 2020
As an update, we received two reviews. Both requested additional data and analysis. This is what peer review is for, to help make better papers. We have carried out these experiments and resubmitted the paper. . I do not think science by press release is suitable for the vast bulk of basic biomedical science and we have avoided and will continue to avoid any comments if and until an accepted paper appears.
James H. Naismith
ORCiDcommented on 03 July, 2020
The revised paper has ended its journey through the peer review system. The now accepted revision is embargoed pending publication. We will distribute reagents in the paper to researchers of course, the coordinates are accessible at the RCSB and the gene products being deposited with Addgene.
View 1 reply
Tahsin Khan
ORCiDreplied on 04 July, 2020
This article is well organised and resourceful for new nanobody derivatives. Congratulations to all authors.
James H. Naismith
ORCiDcommented on 13 July, 2020
The final version now online. https://www.nature.com/articles/s41594-020-0469-6
Tahsin Khan
ORCiDreplied on 04 July, 2020
This article is well organised and resourceful for new nanobody derivatives. Congratulations to all authors.