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- PDB-9yp1: Rabbit Hemorrhagic Disease Virus Czech P domain -

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Basic information

Entry
Database: PDB / ID: 9yp1
TitleRabbit Hemorrhagic Disease Virus Czech P domain
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / lagovirus
Function / homologyCalicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / DI(HYDROXYETHYL)ETHER / Capsid protein
Function and homology information
Biological speciesRabbit hemorrhagic disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKara, D. / Pancera, M. / Hansman, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural insights into a broadly reactive Nanobody that remodels the lagovirus HBGA pocket
Authors: Kara, D. / Pancera, M. / Hassanzadeh, G. / Hartley-Tassell, L. / Haselhorst, T. / von Itzstein, M. / Hansman, G.
History
DepositionOct 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Capsid protein
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,31416
Polymers70,1962
Non-polymers1,11814
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint21 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.968, 51.261, 94.270
Angle α, β, γ (deg.)90.000, 101.050, 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

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Protein , 1 types, 2 molecules BA

#1: Protein Capsid protein


Mass: 35097.875 Da / Num. of mol.: 2 / Fragment: Czech P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabbit hemorrhagic disease virus / Gene: VP60 / Production host: Escherichia coli (E. coli) / References: UniProt: V5K505

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Non-polymers , 5 types, 821 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES (pH 9.0) and 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.37→47.37 Å / Num. obs: 124329 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Χ2: 0.52 / Net I/σ(I): 11.3
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5870 / CC1/2: 0.666 / Rpim(I) all: 0.408 / Rrim(I) all: 0.991 / % possible all: 95.8

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Processing

Software
NameVersionClassification
AUTOMARdata collection
PHENIX1.20.1_4487refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→47.37 Å / SU ML: 0.1302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1715 6215 5 %
Rwork0.1502 118095 -
obs0.1512 124310 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.39 Å2
Refinement stepCycle: LAST / Resolution: 1.37→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 72 807 5769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01165134
X-RAY DIFFRACTIONf_angle_d1.22597039
X-RAY DIFFRACTIONf_chiral_restr0.1074791
X-RAY DIFFRACTIONf_plane_restr0.0115927
X-RAY DIFFRACTIONf_dihedral_angle_d9.291746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.380.28771940.27513687X-RAY DIFFRACTION94.34
1.38-1.40.25332070.23823937X-RAY DIFFRACTION99.5
1.4-1.420.24642050.22223901X-RAY DIFFRACTION99.56
1.42-1.430.24042050.21563896X-RAY DIFFRACTION99.03
1.43-1.450.22252060.20823902X-RAY DIFFRACTION99.71
1.45-1.470.23332050.19643899X-RAY DIFFRACTION99.03
1.47-1.490.20232070.18063926X-RAY DIFFRACTION99.86
1.49-1.520.19862050.18533894X-RAY DIFFRACTION99.39
1.52-1.540.21632070.17883932X-RAY DIFFRACTION99.83
1.54-1.560.21762060.17353906X-RAY DIFFRACTION99.47
1.56-1.590.18942070.17163951X-RAY DIFFRACTION99.88
1.59-1.620.2082060.1683908X-RAY DIFFRACTION99.71
1.62-1.650.19122080.16273970X-RAY DIFFRACTION99.95
1.65-1.690.17962070.14953914X-RAY DIFFRACTION99.93
1.69-1.720.16872060.14523917X-RAY DIFFRACTION99.98
1.72-1.760.1892100.14783987X-RAY DIFFRACTION100
1.76-1.810.21122070.14563922X-RAY DIFFRACTION100
1.81-1.860.17462060.14263930X-RAY DIFFRACTION99.95
1.86-1.910.17522080.14013971X-RAY DIFFRACTION99.98
1.91-1.970.16892080.14453957X-RAY DIFFRACTION100
1.97-2.040.16532070.14053929X-RAY DIFFRACTION99.93
2.04-2.120.15222080.13583945X-RAY DIFFRACTION99.93
2.12-2.220.16282080.13823959X-RAY DIFFRACTION99.98
2.22-2.340.17182100.14073992X-RAY DIFFRACTION99.88
2.34-2.480.15652060.14133914X-RAY DIFFRACTION99.93
2.48-2.680.16662100.14933998X-RAY DIFFRACTION99.98
2.68-2.940.17572090.153973X-RAY DIFFRACTION99.95
2.95-3.370.16112110.14733990X-RAY DIFFRACTION99.79
3.37-4.250.14792100.13244005X-RAY DIFFRACTION99.57
4.25-47.370.13732160.13684083X-RAY DIFFRACTION99.33

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