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- PDB-8en5: Structure of GII.4 norovirus in complex with Nanobody 56 -

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Basic information

Entry
Database: PDB / ID: 8en5
TitleStructure of GII.4 norovirus in complex with Nanobody 56
Components
  • GII.4 P domain
  • Nanobody 56
KeywordsVIRAL PROTEIN / norovirus / Nanobody
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKher, G. / Sabin, C. / Pancera, M. / Koromyslova, A. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: J.Virol. / Year: 2023
Title: Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies.
Authors: Kher, G. / Sabin, C. / Lun, J.H. / Devant, J.M. / Ruoff, K. / Koromyslova, A.D. / von Itzstein, M. / Pancera, M. / Hansman, G.S.
History
DepositionSep 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GII.4 P domain
B: GII.4 P domain
E: Nanobody 56
F: Nanobody 56
C: GII.4 P domain
D: GII.4 P domain
G: Nanobody 56
H: Nanobody 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,95945
Polymers198,5298
Non-polymers2,43037
Water23,7261317
1
A: GII.4 P domain
B: GII.4 P domain
E: Nanobody 56
F: Nanobody 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,01230
Polymers99,2654
Non-polymers1,74726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint54 kcal/mol
Surface area31770 Å2
MethodPISA
2
C: GII.4 P domain
D: GII.4 P domain
G: Nanobody 56
H: Nanobody 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,94715
Polymers99,2654
Non-polymers68311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-0 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.244, 235.384, 70.566
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GII.4 P domain


Mass: 35103.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89
#2: Antibody
Nanobody 56


Mass: 14529.183 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: (10% [w/v] PEG8000 and 0.1 M MES [pH 6.0])

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97658 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97658 Å / Relative weight: 1
ReflectionResolution: 1.6→68.38 Å / Num. obs: 480738 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.633.50.41242518121500.8320.2550.4862.596.9
8.76-235.383.70.037570515450.9820.0230.04326.897.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4oos

4oos


Resolution: 1.6→68.38 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 23818 4.95 %
Rwork0.1859 456920 -
obs0.1875 480738 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.65 Å2 / Biso mean: 28.883 Å2 / Biso min: 11.43 Å2
Refinement stepCycle: final / Resolution: 1.6→68.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13529 0 192 1317 15038
Biso mean--35.68 34.23 -
Num. residues----1736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.3097820.2775150741585694
1.62-1.640.31138160.2695150071582394
1.64-1.660.29647800.2568151581593894
1.66-1.680.27397950.2482150031579895
1.68-1.70.29097350.2407151531588895
1.7-1.720.25788760.2388150341591095
1.72-1.750.27188200.2346151431596395
1.75-1.770.25487690.2267146391540892
1.77-1.80.26567890.2274148571564692
1.8-1.830.25177450.224151431588895
1.83-1.860.25987540.2275153301608496
1.86-1.90.25248090.2181152681607796
1.9-1.930.24677420.2098154101615296
1.93-1.970.24137700.2059153131608396
1.97-2.020.23127980.2029152941609296
2.02-2.060.25567860.1977152021598896
2.06-2.110.22728140.1987150091582394
2.11-2.170.24578230.202147101553392
2.17-2.240.2388370.1883153451618297
2.24-2.310.21478010.1897154631626497
2.31-2.390.22927590.192154241618396
2.39-2.490.23528470.1954153481619597
2.49-2.60.23248330.1957156851651898
2.6-2.740.22567690.1877151291589895
2.74-2.910.23357720.192153131608596
2.91-3.130.24817800.1842156571643798
3.13-3.450.1977960.1809157131650998
3.45-3.950.18888360.1707153191615596
3.95-4.970.17057910.1385154701626197
4.97-68.380.17767940.1539153071610196

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