7Z85
CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-B5 nanobody complex
Summary for 7Z85
| Entry DOI | 10.2210/pdb7z85/pdb |
| Related | 7Z6V 7Z7X |
| EMDB information | 14543 |
| Descriptor | Spike glycoprotein,Fibritin, Nanobody H11-B5, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total) |
| Functional Keywords | complex, spike glycoprotein, nanobody h11-b5, antiviral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 More |
| Total number of polymer chains | 6 |
| Total formula weight | 478755.09 |
| Authors | Weckener, M.,Naismith, J.H. (deposition date: 2022-03-16, release date: 2022-07-13, Last modification date: 2024-10-23) |
| Primary citation | Mikolajek, H.,Weckener, M.,Brotzakis, Z.F.,Huo, J.,Dalietou, E.V.,Le Bas, A.,Sormanni, P.,Harrison, P.J.,Ward, P.N.,Truong, S.,Moynie, L.,Clare, D.K.,Dumoux, M.,Dormon, J.,Norman, C.,Hussain, N.,Vogirala, V.,Owens, R.J.,Vendruscolo, M.,Naismith, J.H. Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes. Proc.Natl.Acad.Sci.USA, 119:e2205412119-e2205412119, 2022 Cited by PubMed Abstract: Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein. PubMed: 35858383DOI: 10.1073/pnas.2205412119 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.1 Å) |
Structure validation
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