9DQC | pdb_00009dqc

Hare calicivirus protruding domain and A-trisaccharide complex

PDB DOI: https://doi.org/10.2210/pdb9DQC/pdb

Classification: VIRAL PROTEIN
Organism(s): Hare calicivirus Australia-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-23 Released: 2024-10-30
Deposition Author(s): Reese, T., Pancera, M., Hansman, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.178 (Depositor), 0.178 (DCC)
R-Value Work:
0.155 (Depositor), 0.155 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural analysis of a non-pathogenic hare calicivirus capsid bound to a histo-blood group antigen co-factor.

Hansman, G.S., Reese, T., Pancera, M., Rudd, P.A., Masic, V., Haselhorst, T., von Itzstein, M.

(2024) J Virol 98: e0167524-e0167524

PubMed: 39513720 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/jvi.01675-24
Primary Citation of Related Structures:
9DQC, 9DR0

Organizational Affiliation

Institute for Biomedicine and Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.

Macromolecule Content

Total Structure Weight: 69.79 kDa
Atom Count: 5,620
Modeled Residue Count: 664
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hare calicivirus protruding domain	A, B	332	Hare calicivirus Australia-1	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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C, D	3		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G15611BA GlyCosmos: G15611BA GlyGen: G15611BA

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.178 (Depositor), 0.178 (DCC)
R-Value Work: 0.155 (Depositor), 0.155 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.11	α = 90
b = 82.526	β = 90.96
c = 74.331	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-10-30
Type: Initial release
Version 1.1: 2025-05-14
Changes: Database references

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.