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- PDB-9dqc: Hare calicivirus protruding domain and A-trisaccharide complex -

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Basic information

Entry
Database: PDB / ID: 9dqc
TitleHare calicivirus protruding domain and A-trisaccharide complex
ComponentsHare calicivirus protruding domain
KeywordsVIRAL PROTEIN / lagovirus / hare calicivirus
Biological speciesHare calicivirus Australia-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsReese, T. / Pancera, M. / Hansman, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2024
Title: Structural analysis of a non-pathogenic hare calicivirus capsid bound to a histo-blood group antigen co-factor.
Authors: Hansman, G.S. / Reese, T. / Pancera, M. / Rudd, P.A. / Masic, V. / Haselhorst, T. / von Itzstein, M.
History
DepositionSep 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hare calicivirus protruding domain
B: Hare calicivirus protruding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7896
Polymers68,6062
Non-polymers1,1834
Water12,791710
1
A: Hare calicivirus protruding domain
B: Hare calicivirus protruding domain
hetero molecules

hetero molecules

hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7896
Polymers68,6062
Non-polymers1,1834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4510 Å2
ΔGint8 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.110, 82.526, 74.331
Angle α, β, γ (deg.)90.000, 90.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Hare calicivirus protruding domain


Mass: 34302.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hare calicivirus Australia-1 / Production host: Escherichia coli (E. coli)
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 20% w/v PEG3350, 60-molar excess of A-trisaccharide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.42→44.62 Å / Num. obs: 123900 / % possible obs: 99.6 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.9
Reflection shellResolution: 1.42→1.45 Å / Num. unique obs: 12078 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→44.62 Å / SU ML: 0.1866 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1776 1996 1.61 %
Rwork0.1552 121904 -
obs0.1556 123900 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.33 Å2
Refinement stepCycle: LAST / Resolution: 1.42→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 80 710 5620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095036
X-RAY DIFFRACTIONf_angle_d1.02746916
X-RAY DIFFRACTIONf_chiral_restr0.0845804
X-RAY DIFFRACTIONf_plane_restr0.0108906
X-RAY DIFFRACTIONf_dihedral_angle_d6.4262719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.35631320.34678457X-RAY DIFFRACTION97.12
1.46-1.50.31971460.3088692X-RAY DIFFRACTION99.94
1.5-1.540.30451540.27468664X-RAY DIFFRACTION99.86
1.54-1.590.26481360.24848684X-RAY DIFFRACTION99.94
1.59-1.650.22971420.22548742X-RAY DIFFRACTION99.93
1.65-1.720.20031430.19438701X-RAY DIFFRACTION99.83
1.72-1.790.2051410.1658719X-RAY DIFFRACTION99.88
1.79-1.890.1881400.15098699X-RAY DIFFRACTION99.9
1.89-2.010.15391410.1398699X-RAY DIFFRACTION99.88
2.01-2.160.17451450.13588740X-RAY DIFFRACTION99.87
2.16-2.380.16551420.13448734X-RAY DIFFRACTION99.89
2.38-2.720.15271420.13788762X-RAY DIFFRACTION99.88
2.72-3.430.15511470.14278788X-RAY DIFFRACTION99.88
3.43-44.620.15331450.12718823X-RAY DIFFRACTION99.31

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