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Structure paper

TitleStructure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Journal, issue, pagesScience, Vol. 371, Issue 6530, Year 2021
Publish dateFeb 12, 2021
AuthorsPaul-Albert Koenig / Hrishikesh Das / Hejun Liu / Beate M Kümmerer / Florian N Gohr / Lea-Marie Jenster / Lisa D J Schiffelers / Yonas M Tesfamariam / Miki Uchima / Jennifer D Wuerth / Karl Gatterdam / Natalia Ruetalo / Maria H Christensen / Caroline I Fandrey / Sabine Normann / Jan M P Tödtmann / Steffen Pritzl / Leo Hanke / Jannik Boos / Meng Yuan / Xueyong Zhu / Jonathan L Schmid-Burgk / Hiroki Kato / Michael Schindler / Ian A Wilson / Matthias Geyer / Kerstin U Ludwig / B Martin Hällberg / Nicholas C Wu / Florian I Schmidt /
PubMed AbstractThe pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost ...The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.
External linksScience / PubMed:33436526 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.87 - 4.01 Å
Structure data

11978

7b14

EMDB-11978, PDB-7b14:
Nanobody E bound to Spike-RBD in a localized reconstruction
Method: EM (single particle) / Resolution: 3.79 Å

11980

7b17

EMDB-11980, PDB-7b17:
SARS-CoV-spike RBD bound to two neutralising nanobodies.
Method: EM (single particle) / Resolution: 4.01 Å

11981

7b18

EMDB-11981, PDB-7b18:
SARS-CoV-spike bound to two neutralising nanobodies
Method: EM (single particle) / Resolution: 2.62 Å

23018

7ksg

EMDB-23018, PDB-7ksg:
SARS-CoV-2 spike in complex with nanobodies E
Method: EM (single particle) / Resolution: 3.33 Å

PDB-7kn5:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-7kn6:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-7kn7:
Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3
Method: X-RAY DIFFRACTION / Resolution: 2.73 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
  • camelus bactrianus (Bactrian camel)
  • vicugna pacos (alpaca)
  • lama glama (llama)
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / spike glycoprotein / SARS-CoV-2 / nanobody / VIRAL PROTEIN/IMMUNE SYSTEM / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / Nanobody-antigen complex / single-domain antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex / Antibody / spike protein / VIRUS

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