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- PDB-8en1: Structure of GII.4 norovirus in complex with Nanobody 30 -

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Basic information

Entry
Database: PDB / ID: 8en1
TitleStructure of GII.4 norovirus in complex with Nanobody 30
Components
  • GII.4 P domain
  • Nanobody 30
KeywordsVIRAL PROTEIN / norovirus / Nanobody / inhibitor
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / VP1
Function and homology information
Biological speciesNorovirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Sep 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 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GII.4 P domain
B: GII.4 P domain
C: Nanobody 30
D: Nanobody 30


Theoretical massNumber of molelcules
Total (without water)100,8144
Polymers100,8144
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.767, 62.443, 121.396
Angle α, β, γ (deg.)90.000, 101.240, 90.000
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

21B-702-

HOH

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Components

#1: Protein GII.4 P domain


Mass: 35103.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89
#2: Antibody Nanobody 30


Mass: 15303.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: (0.2 M calcium chloride and 20% [w/v] PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.4→57.75 Å / Num. obs: 34103 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.082 / Rrim(I) all: 0.187 / Net I/σ(I): 5.5 / Num. measured all: 169376 / Scaling rejects: 605
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
2.4-2.494.60.5541617235380.7480.2920.6292.198.7
8.97-57.754.90.09733646930.9850.0450.1088.899

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X7E

4x7e


Resolution: 2.4→57.75 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 3844 5.86 %
Rwork0.2066 61742 -
obs0.2099 34056 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.38 Å2 / Biso mean: 28.3294 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 2.4→57.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 0 273 7163
Biso mean---27.28 -
Num. residues----877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.430.36271450.29732230237597
2.43-2.460.31981290.27322226235597
2.46-2.50.34851480.26722295244399
2.5-2.530.24541450.26342285243099
2.53-2.570.3771330.265923502483100
2.57-2.610.331510.26212261241299
2.61-2.650.26551350.2682289242499
2.65-2.70.37341420.262923162458100
2.7-2.750.28391560.268123062462100
2.75-2.80.34191330.24812320245399
2.8-2.860.31161360.251723112447100
2.86-2.920.2971450.24662273241899
2.92-2.990.33911370.24782294243199
2.99-3.060.24011480.22892295244399
3.06-3.140.2711510.22542269242097
3.14-3.240.30161340.20872230236497
3.24-3.340.25131430.20322942437100
3.34-3.460.26051460.211123352481100
3.46-3.60.24641370.191522822419100
3.6-3.760.25621420.19632317245999
3.76-3.960.21871460.17842263240999
3.96-4.210.23011410.16352329247099
4.21-4.530.22181480.14752265241398
4.54-4.990.25121400.1482220236098
4.99-5.710.18731540.17142328248299
5.71-7.190.21831440.18392288243299
7.2-57.750.23151350.18372271240698

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