9YP2 | pdb_00009yp2

Structure of HaCV P domain in complex with Nanobody 7

• PDB DOI: https://doi.org/10.2210/pdb9YP2/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Hare calicivirus, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-13 Released: 2025-12-03 
• Deposition Author(s): Kara, D., Pancera, M., Hansman, G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Models: experimental

Literature

Structural insights into a broadly reactive nanobody that binds pathogenic and non-pathogenic lagoviruses.

Kara, D., Pancera, M., Hassanzadeh-Ghassabeh, G., Schoonooghe, S., Masic, V., Hartley-Tassell, L., Mishra, B.P., Ve, T., Haselhorst, T., von Itzstein, M., Hansman, G.S.

(2026) J Virol 100: e0199025-e0199025

• PubMed: 41504443 
• DOI: https://doi.org/10.1128/jvi.01990-25
• Primary Citation Related Structures: 
  9YP1, 9YP2

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Organizational Affiliation: 
• Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
VIB Nanobody VHH Core, Vrije Universiteit Brussel, Brussels, Belgium.
Institute for Biomedicine and Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.29 kDa 
• Atom Count: 6,812 
• Modeled Residue Count: 871 
• Deposited Residue Count: 900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, C [auth B]	339	Hare calicivirus	Mutation(s): 0
UniProt
Find proteins for A0A4D6I9J0 (Hare calicivirus Australia-2) Explore A0A4D6I9J0  Go to UniProtKB:  A0A4D6I9J0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 7	B [auth C], D	111	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.223 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.25	α = 90
b = 73.51	β = 94.11
c = 59.25	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Kara, D., Pancera, M., Hansman, G.

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Funding Organization	Location	Grant Number
Other government	Australia	24070

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Database references