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- PDB-6h9v: Crystal structure of deaminated P domain from norovirus strain Sa... -

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Basic information

Entry
Database: PDB / ID: 6h9v
TitleCrystal structure of deaminated P domain from norovirus strain Saga GII-4 in complex with Fuc
ComponentsVP1
KeywordsVIRAL PROTEIN / VIRAL CAPSID PROTEIN / PROTRUDING DOMAIN / ISOASPARTATE / ISOPEPTIDE / FUCOSE / GLYCAN / RECEPTOR
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
methyl alpha-L-fucopyranoside / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII-4/Saga4/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.52 Å
AuthorsMeyer, P.H.O. / Blaum, B.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBL1294/3-1 Germany
CitationJournal: Nat Commun / Year: 2019
Title: A post-translational modification of human Norovirus capsid protein attenuates glycan binding.
Authors: Mallagaray, A. / Creutznacher, R. / Dulfer, J. / Mayer, P.H.O. / Grimm, L.L. / Orduna, J.M. / Trabjerg, E. / Stehle, T. / Rand, K.D. / Blaum, B.S. / Uetrecht, C. / Peters, T.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4896
Polymers68,0842
Non-polymers4054
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: P-domain forms homodimer also in the context of the viral capsid
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-30 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.290, 83.950, 65.130
Angle α, β, γ (deg.)90.00, 95.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VP1


Mass: 34042.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: E373 is converted to IAS (isoaspartate) / Source: (gene. exp.) Norovirus Hu/GII-4/Saga4/2006/JP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5BTR7
#2: Sugar ChemComp-MFU / methyl alpha-L-fucopyranoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Mg formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.542 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.52→39.58 Å / Num. obs: 88343 / % possible obs: 99 % / Redundancy: 4.62 % / Biso Wilson estimate: 21.52 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.18
Reflection shellResolution: 1.52→1.56 Å / CC1/2: 0.316 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementResolution: 1.52→39.577 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1828 4418 5 %
Rwork0.1473 --
obs0.1491 88339 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→39.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4746 0 2 616 5364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085202
X-RAY DIFFRACTIONf_angle_d0.9327153
X-RAY DIFFRACTIONf_dihedral_angle_d11.0113051
X-RAY DIFFRACTIONf_chiral_restr0.061799
X-RAY DIFFRACTIONf_plane_restr0.007950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.53730.35831460.3292773X-RAY DIFFRACTION100
1.5373-1.55540.36371480.31482809X-RAY DIFFRACTION99
1.5554-1.57440.32991460.27852763X-RAY DIFFRACTION100
1.5744-1.59430.27191490.27032847X-RAY DIFFRACTION99
1.5943-1.61530.28421480.25152804X-RAY DIFFRACTION99
1.6153-1.63740.2891470.24122799X-RAY DIFFRACTION99
1.6374-1.66080.28971460.22682771X-RAY DIFFRACTION99
1.6608-1.68560.24461470.20752788X-RAY DIFFRACTION99
1.6856-1.71190.23891470.20682803X-RAY DIFFRACTION99
1.7119-1.740.23751470.18662777X-RAY DIFFRACTION99
1.74-1.770.21711450.18722752X-RAY DIFFRACTION99
1.77-1.80220.22561470.18222795X-RAY DIFFRACTION98
1.8022-1.83690.21461450.1652766X-RAY DIFFRACTION98
1.8369-1.87440.20361450.16412759X-RAY DIFFRACTION98
1.8744-1.91510.16641470.14992780X-RAY DIFFRACTION98
1.9151-1.95970.18891410.15052681X-RAY DIFFRACTION95
1.9597-2.00870.17861470.14332801X-RAY DIFFRACTION99
2.0087-2.0630.17431470.14412796X-RAY DIFFRACTION100
2.063-2.12370.16251490.12982824X-RAY DIFFRACTION100
2.1237-2.19220.17781480.1322819X-RAY DIFFRACTION100
2.1922-2.27060.15731510.13192859X-RAY DIFFRACTION100
2.2706-2.36150.17621480.13652808X-RAY DIFFRACTION100
2.3615-2.46890.19291490.1352828X-RAY DIFFRACTION100
2.4689-2.59910.18091480.14212815X-RAY DIFFRACTION100
2.5991-2.76190.17611480.14422823X-RAY DIFFRACTION100
2.7619-2.9750.20351500.14752835X-RAY DIFFRACTION100
2.975-3.27430.16151450.13072759X-RAY DIFFRACTION98
3.2743-3.74780.16651430.13062719X-RAY DIFFRACTION96
3.7478-4.72060.13321510.11022865X-RAY DIFFRACTION100
4.7206-39.59020.17781530.14652903X-RAY DIFFRACTION100
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)
10.4974-0.06680.10320.4029-0.00460.34960.01120.01180.0129-0.0115-0.01260.05450.0037-0.008800.15880.0017-0.00070.1582-0.00930.1853-0.5043-15.389660.3178
20.20040.00380.10620.28390.03270.11480.00030.03150.0224-0.06690.02580.0857-0.12-0.060700.19520.0053-0.02120.17340.01190.1814-3.8892-5.301748.6022
30.28980.0945-0.15750.34320.14410.18220.0247-0.03210.0840.02670.0260.0773-0.0659-0.013300.17850.0070.00560.1656-0.01070.17842.0179-7.218568.4387
40.03580.0610.00310.25690.08580.2675-0.02550.00710.00580.01770.040.01480.0480.040100.17520.00890.00870.1698-0.00120.181611.5042-22.312569.1644
50.1403-0.17-0.06110.16460.02490.1987-0.1437-0.13520.35650.0590.0964-0.0536-0.14620.115600.2165-0.0143-0.02610.2011-0.01810.230715.1664-19.701777.5313
60.06380.00140.05390.0978-0.00950.03950.0011-0.1123-0.02370.1543-0.1038-0.20760.04630.0957-0.00010.25910.0102-0.02250.2369-0.00790.21513.9583-28.409182.0269
70.46640.2917-0.15740.48920.00280.1437-0.02350.02220.0218-0.02680.0501-0.0043-0.04270.069800.1745-0.016-0.00140.2045-0.01420.166317.5337-21.283746.9857
80.38930.0818-0.06510.23190.32330.3767-0.04280.05460.0352-0.10730.0274-0.0625-0.11930.0051-00.2106-0.0348-0.00050.17840.00440.165716.6399-7.978642.3638
90.0149-0.0370.0340.0581-0.03350.06390.03920.09350.001-0.14430.0273-0.09150.04250.138700.226-0.02070.04850.2729-0.03380.219623.8012-23.457335.1306
100.3989-0.1946-0.12620.64210.07330.5357-0.06250.0295-0.0835-0.03230.05030.03750.05340.031700.16920.00340.00420.1831-0.00950.18185.9306-38.35145.3338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 222 through 323 )
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 380 )
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 437 )
4X-RAY DIFFRACTION4chain 'A' and (resid 438 through 484 )
5X-RAY DIFFRACTION5chain 'A' and (resid 485 through 513 )
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 530 )
7X-RAY DIFFRACTION7chain 'B' and (resid 224 through 323 )
8X-RAY DIFFRACTION8chain 'B' and (resid 324 through 400 )
9X-RAY DIFFRACTION9chain 'B' and (resid 401 through 420 )
10X-RAY DIFFRACTION10chain 'B' and (resid 421 through 530 )

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