4X7F

Crystal structure of norovirus GII.10 P domain in complex with Nano-25

DOI: 10.2210/pdb4X7F/pdb

Classification: VIRAL PROTEIN
Organism(s): Vicugna pacos, Norwalk virus
Expression System: Escherichia coli, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-09 Released: 2014-12-31
Deposition Author(s): Koromyslova, A.D., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.187
R-Value Work: 0.160
R-Value Observed: 0.161

wwPDB Validation3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Nanobody binding to a conserved epitope promotes norovirus particle disassembly.

Koromyslova, A.D., Hansman, G.S.

(2015) J Virol 89: 2718-2730

PubMed: 25520510 Search on PubMedSearch on PubMed Central
DOI: 10.1128/JVI.03176-14
Structures With Same Primary Citation

PubMed Abstract:

Human noroviruses are icosahedral single-stranded RNA viruses. The capsid protein is divided into shell (S) and protruding (P) domains, which are connected by a flexible hinge region. There are numerous genetically and antigenically distinct noroviruses, and the dominant strains evolve every other year. Vaccine and antiviral development is hampered by the difficulties in growing human norovirus in cell culture and the continually evolving strains. Here, we show the X-ray crystal structures of human norovirus P domains in complex with two different nanobodies. One nanobody, Nano-85, was broadly reactive, while the other, Nano-25, was strain specific. We showed that both nanobodies bound to the lower region on the P domain and had nanomolar affinities. The Nano-85 binding site mainly comprised highly conserved amino acids among the genetically distinct genogroup II noroviruses. Several of the conserved residues also were recognized by a broadly reactive monoclonal antibody, which suggested this region contained a dominant epitope. Superposition of the P domain nanobody complex structures into a cryoelectron microscopy particle structure revealed that both nanobodies bound at occluded sites on the particles. The flexible hinge region, which contained ~10 to 12 amino acids, likely permitted a certain degree of P domain movement on the particles in order to accommodate the nanobodies. Interestingly, the Nano-85 binding interaction with intact particles caused the particles to disassemble in vitro. Altogether, these results suggested that the highly conserved Nano-85 binding epitope contained a trigger mechanism for particle disassembly. Principally, this epitope represents a potential site of norovirus vulnerability.

Organizational Affiliation:

Schaller Research Group at the University of Heidelberg and the DKFZ, Germany, Heidelberg, Germany, and Department of Infectious Diseases, Virology, University of Heidelberg, Germany, Heidelberg, Germany g.hansman@dkfz.de.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nano-25 Nanobody	C, D	119	Vicugna pacos	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Capsid protein	A, B	315	Norwalk virus	Mutation(s): 0
Find proteins for Q5F4T5 (Norwalk virus) Go to UniProtKB: Q5F4T5
Protein Feature View Full Protein Feature View for Q5F4T5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download CCD File	A	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
IMD Query on IMD Download CCD File	B, C	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Ligand Interaction
EDO Query on EDO Download CCD File	A, B, C, D	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download CCD File	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction