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- PDB-5o02: GII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4 -

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Basic information

Entry
Database: PDB / ID: 5o02
TitleGII.17 Kawasaki323 protruding domain in complex with Nanobody Nano-4
Components
  • Capsid protein
  • Nanobody (VHH) Nano-4
KeywordsVIRAL PROTEIN / Norovirus / Protruding domain / capsid / VHH / Nanobody
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Capsid protein
Similarity search - Component
Biological speciesNorovirus 13-BH-1/2013/GII.17
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsKoromyslova, A.D. / Hansman, G.S.
CitationJournal: PLoS Pathog. / Year: 2017
Title: Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization.
Authors: Koromyslova, A.D. / Hansman, G.S.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
C: Nanobody (VHH) Nano-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1149
Polymers47,6732
Non-polymers4417
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint17 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.470, 64.040, 70.030
Angle α, β, γ (deg.)90.000, 97.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-760-

HOH

21A-1018-

HOH

31A-1033-

HOH

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Components

#1: Protein Capsid protein


Mass: 34085.926 Da / Num. of mol.: 1 / Fragment: UNP residues 225-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus 13-BH-1/2013/GII.17 / Variant: Kawasaki323 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A7CJV4
#2: Antibody Nanobody (VHH) Nano-4


Mass: 13586.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: Phen6C / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium acetate, 10% (w/v) PEG8000, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.69→45.06 Å / Num. obs: 55894 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.165 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.082 / Χ2: 1.024 / Net I/σ(I): 11.55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.69-1.82.930.4272.2684120.8490.52190.2
1.8-1.923.2980.2713.9485240.9280.32497.6
1.92-2.073.310.176.2879890.970.20498.1
2.07-2.273.2240.1189.1973920.9810.14298.3
2.27-2.542.9830.08511.9266410.9870.10497.8
2.54-2.933.2520.06116.8559150.9940.07397.8
2.93-3.593.2190.04423.4849550.9960.05397.5
3.59-5.052.960.03328.4538440.9970.04196.5
5.05-45.063.3780.03231.5122220.9970.03897.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.69 Å45.06 Å
Translation7.06 Å45.06 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F4M and 4X4C

5f4m

4x4c


Resolution: 1.72→45.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.49
RfactorNum. reflection% reflection
Rfree0.1805 2703 5 %
Rwork0.1503 --
obs0.1518 54046 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.32 Å2 / Biso mean: 20.9462 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.72→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 29 515 3869
Biso mean--43.64 33 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063628
X-RAY DIFFRACTIONf_angle_d1.0514960
X-RAY DIFFRACTIONf_chiral_restr0.045521
X-RAY DIFFRACTIONf_plane_restr0.005672
X-RAY DIFFRACTIONf_dihedral_angle_d12.0711322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.75130.3031400.26052665280597
1.7513-1.7850.23821410.23642665280697
1.785-1.82140.25731400.20242664280497
1.8214-1.8610.23921420.19162701284398
1.861-1.90430.21931410.18032681282298
1.9043-1.95190.21981430.17012707285098
1.9519-2.00470.22681410.16512685282698
2.0047-2.06370.20021430.16172711285498
2.0637-2.13030.19371440.15242732287698
2.1303-2.20640.18321410.14962692283398
2.2064-2.29480.171420.15062696283898
2.2948-2.39920.19331430.15182724286798
2.3992-2.52570.18461420.15412685282798
2.5257-2.68390.21421430.15542723286697
2.6839-2.89110.181420.15262700284298
2.8911-3.1820.16551440.14452725286998
3.182-3.64220.15011420.13532698284097
3.6422-4.58810.14081410.11622690283196
4.5881-45.07580.15111480.13592799294798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70550.1930.21891.26860.89181.31690.01080.0943-0.0767-0.06860.0198-0.10190.03610.0684-0.00970.0770.00890.01620.10920.00020.0876-15.9811-63.1776204.5607
21.36890.4170.22850.56650.16840.79230.03420.1012-0.2507-0.07780.0166-0.11180.04630.0486-0.04430.09680.02580.01120.1024-0.02860.1143-14.2817-73.4175201.6517
30.75180.64710.28371.55440.33940.44610.0173-0.02250.01190.0554-0.0186-0.0139-0.0030.0332-0.00050.0779-0.00220.01290.11240.00050.0621-13.7728-51.0198219.7183
43.29044.7882.98826.96744.34832.7137-0.55160.73420.2049-0.72960.35430.0809-0.69630.75270.32430.2763-0.03920.04470.25070.00060.16712.3049-26.7987223.5207
51.7354-1.6663-1.42026.23-2.54314.4885-0.34010.06080.3423-0.00240.0926-0.1771-0.60620.78050.22760.1764-0.0715-0.02190.2236-0.01190.148912.6698-21.4852244.088
67.71426.39417.19825.33536.01396.7805-0.0396-0.01590.2119-0.2451-0.02590.0751-0.3148-0.07130.1460.19390.027-0.00750.1402-0.02420.1191-0.3918-23.2417230.71
78.6237-3.08297.87482.9436-3.58998.6309-0.22960.01160.08920.03020.0998-0.0489-0.2639-0.19020.14650.11570.00410.01740.1196-0.03890.0728-3.5198-31.6177232.1295
86.59340.35170.12062.2778-0.58454.9444-0.1001-0.4329-0.12710.34680.0308-0.56680.36480.3240.05170.16860.019-0.04610.1199-0.00260.14384.0836-36.6521239.5696
94.1896-0.05455.48943.1152-0.00527.25480.1004-0.3574-0.0430.2317-0.06650.21460.165-0.494-0.04030.13350.00980.02910.1734-0.01030.112-7.2286-30.7435242.008
104.58830.46740.20594.39492.64981.5987-0.0845-0.4213-0.05690.1681-0.07880.25490.0409-0.3191-0.00820.12010.00610.01770.1445-0.02880.0841-3.4357-25.3464242.577
114.2462-2.88555.66953.0896-3.55727.7358-0.13220.16860.2574-0.0416-0.00350.0528-0.33390.17940.1940.21750.0211-0.04630.18050.00220.1434-2.4684-21.686234.6013
123.65841.70672.54891.75081.70932.88130.0103-0.1503-0.05760.138-0.03260.02340.0563-0.050900.11960.01720.0190.1109-0.00090.0566-1.319-33.0757237.2116
133.07442.18831.78694.12972.19934.6125-0.28520.1369-0.0921-0.28440.2012-0.22840.00150.37460.09320.10420.01660.01660.0923-0.00330.06872.0218-35.1873227.9151
147.5453-0.41264.59467.8913-2.09183.2285-0.10210.07420.0365-0.05660.3547-0.44-0.50180.985-0.17660.10910.0058-0.00110.2668-0.05490.131714.3607-26.792240.6376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 315 )A225 - 315
2X-RAY DIFFRACTION2chain 'A' and (resid 316 through 426 )A316 - 426
3X-RAY DIFFRACTION3chain 'A' and (resid 427 through 528 )A427 - 528
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 7 )C1 - 7
5X-RAY DIFFRACTION5chain 'C' and (resid 8 through 17 )C8 - 17
6X-RAY DIFFRACTION6chain 'C' and (resid 18 through 28 )C18 - 28
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 39 )C29 - 39
8X-RAY DIFFRACTION8chain 'C' and (resid 40 through 51 )C40 - 51
9X-RAY DIFFRACTION9chain 'C' and (resid 52 through 64 )C52 - 64
10X-RAY DIFFRACTION10chain 'C' and (resid 65 through 73 )C65 - 73
11X-RAY DIFFRACTION11chain 'C' and (resid 74 through 83 )C74 - 83
12X-RAY DIFFRACTION12chain 'C' and (resid 84 through 108 )C84 - 108
13X-RAY DIFFRACTION13chain 'C' and (resid 109 through 117 )C109 - 117
14X-RAY DIFFRACTION14chain 'C' and (resid 118 through 124 )C118 - 124

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