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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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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.01675-24
Primary Citation 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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4D6I9J0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.