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

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
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into a broadly reactive Nanobody that remodels the lagovirus HBGA pocket

Kara, D., Pancera, M., Hassanzadeh, G., Hartley-Tassell, L., Haselhorst, T., von Itzstein, M., Hansman, G.

To be published.

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4D6I9J0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 7	B [auth C], D	111	Vicugna pacos	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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

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Entry History & Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Australia	24070

Revision History (Full details and data files)

Version 1.0: 2025-12-03
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.