Structure Determination of an Fab Fragment that Neutralizes Human Rhinovirus 14 and Analysis of the Fab-Virus Complex

1994 ◽  
Vol 240 (2) ◽  
pp. 127-137 ◽  
Author(s):  
Hansong Liu ◽  
Thomas J. Smith ◽  
Wai-ming Lee ◽  
Anne G. Mosser ◽  
Roland R. Rueckert ◽  
...  
Keyword(s):  
Structure Determination ◽  
Human Rhinovirus ◽  
Fab Fragment ◽  
Virus Complex

Structure Determination of Antiviral Compound SCH 38057 Complexed with Human Rhinovirus 14

1993 ◽  
Vol 230 (3) ◽  
pp. 857-867 ◽  
Author(s):  
Anqiang Zhang ◽  
Raymond G. Nanni ◽  
Thomas Li ◽  
Gail Ferstandig Arnold ◽  
Deena A. Oren ◽  
...  
Keyword(s):  
Structure Determination ◽  
Human Rhinovirus ◽  
Antiviral Compound

scholarly journals Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

2021 ◽  
Vol 118 (41) ◽  
pp. e2115001118
Author(s):  
Xudong Wu ◽  
Tom A. Rapoport
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
De Novo ◽  
Binding Protein ◽  
Protein A ◽  
Fab Fragment ◽  
Binding Domains ◽  
Binding Interface ◽  
Small Proteins

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody–target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

The structure determination of a common cold virus, human rhinovirus 14

1987 ◽  
Vol 43 (3) ◽  
pp. 346-361 ◽  
Author(s):  
E. Arnold ◽  
G. Vriend ◽  
M. Luo ◽  
J. P. Griffith ◽  
G. Kamer ◽  
...  
Keyword(s):  
Structure Determination ◽  
Common Cold ◽  
Human Rhinovirus

scholarly journals Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

2021 ◽  
Author(s):  
Xudong Wu ◽  
Tom A Rapoport
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
De Novo ◽  
Binding Protein ◽  
Protein A ◽  
Fab Fragment ◽  
Binding Domains ◽  
Binding Interface ◽  
Small Proteins

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: (1) a Fab-fragment of an antibody directed against the nanobody, and (2) a nanobody-binding protein A fragment fused to maltose-binding protein and Fab-binding domains. The overall ensemble of ~120 kDa, called Legobody, does not perturb the nanobody-target interaction and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23 kDa membrane protein, resulting in a map at 3.2 Angstrom overall resolution with density sufficient for de novo model building, and for the 22 kDa RBD of SARS-CoV2 spike protein, resulting in a map at 3.6 Angstrom overall resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

Structure determination of sodium nitrate near the order-disorder phase transition

1984 ◽  
Vol 45 (8) ◽  
pp. 1317-1327 ◽  
Author(s):  
J. Lefebvre ◽  
R. Fouret ◽  
C.M.E. Zeyen
Keyword(s):  
Phase Transition ◽  
Sodium Nitrate ◽  
Structure Determination ◽  
Disorder Phase Transition

Ab initio structure determination of cytochrome c6 by combined reciprocal space-real space approach

2003 ◽  
Vol 218 (1) ◽  
Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee
Keyword(s):  
Cytochrome C ◽  
Ab Initio ◽  
Structure Determination ◽  
Direct Method ◽  
Real Space ◽  
Reciprocal Space ◽  
Cytochrome C6 ◽  
Ab Initio Structure ◽  
Space Approach

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c

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