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- PDB-5omn: GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27 -

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Basic information

Entry
Database: PDB / ID: 5omn
TitleGII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27
Components
  • Capsid proteinCapsid
  • Nanobody (VHH) Nano-27
KeywordsVIRAL PROTEIN / Norovirus / Protruding domain / capsid / VHH / Nanobody
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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 ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / 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
Biological speciesNorwalk virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.682 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
DepositionAug 1, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Capsid protein
C: Nanobody (VHH) Nano-27


Theoretical massNumber of molelcules
Total (without water)47,9002
Polymers47,9002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-0 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.449, 167.449, 143.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Capsid protein / Capsid


Mass: 34506.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Antibody Nanobody (VHH) Nano-27


Mass: 13392.866 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

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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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97319 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 2.68→48.338 Å / Num. obs: 33589 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 19.296 % / Biso Wilson estimate: 65.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.154 / Χ2: 1.156 / Net I/σ(I): 20.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.68-2.8419.3411.9581.6551750.7442.0197
2.84-3.0419.9641.1393.1550240.9171.169100
3.04-3.2818.8580.4957.0447120.9830.509100
3.28-3.5920.7270.27513.0843320.9940.282100
3.59-4.0219.8590.14423.0139630.9980.148100
4.02-4.6318.350.0836.9535270.9990.082100
4.63-5.6619.1670.06445.3930070.9990.066100
5.66-7.9518.6230.05650.423950.9990.057100
7.95-48.33816.1150.03668.1314540.9990.03799.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU, 4X7E

3onu

4x7e


Resolution: 2.682→48.338 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.02
RfactorNum. reflection% reflection
Rfree0.2625 1680 5 %
Rwork0.2348 --
obs0.2361 33568 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.44 Å2 / Biso mean: 68.2221 Å2 / Biso min: 21.44 Å2
Refinement stepCycle: final / Resolution: 2.682→48.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 0 0 3218
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023304
X-RAY DIFFRACTIONf_angle_d0.4774520
X-RAY DIFFRACTIONf_chiral_restr0.021508
X-RAY DIFFRACTIONf_plane_restr0.002593
X-RAY DIFFRACTIONf_dihedral_angle_d9.3391162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6823-2.76130.43951300.36782458258894
2.7613-2.85040.40231370.32626142751100
2.8504-2.95230.3161380.302926192757100
2.9523-3.07040.36721380.282926172755100
3.0704-3.21020.30571400.274426502790100
3.2102-3.37940.26861380.251926232761100
3.3794-3.5910.26761400.23926502790100
3.591-3.86820.23861400.228226632803100
3.8682-4.25720.2471410.217226772818100
4.2572-4.87280.2311410.194926872828100
4.8728-6.13720.2181440.214427352879100
6.1372-48.34620.25641530.227528953048100

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