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- PDB-6nir: Crystal structure of a GII.4 norovirus HOV protease -

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Basic information

Entry
Database: PDB / ID: 6nir
TitleCrystal structure of a GII.4 norovirus HOV protease
Components
  • HOV protease
  • HOV protease fragment
KeywordsVIRAL PROTEIN / norovirus / protease
Function / homologyTrypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsPrasad, B.V.V. / Hu, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)PO1 AI057788 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: J. Virol. / Year: 2019
Title: GII.4 Norovirus Protease Shows pH-Sensitive Proteolysis with a Unique Arg-His Pairing in the Catalytic Site.
Authors: Viskovska, M.A. / Zhao, B. / Shanker, S. / Choi, J.M. / Deng, L. / Song, Y. / Palzkill, T. / Hu, L. / Estes, M.K. / Venkataram Prasad, B.V.
History
DepositionDec 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
A: HOV protease
B: HOV protease
C: HOV protease
D: HOV protease
X: HOV protease fragment


Theoretical massNumber of molelcules
Total (without water)78,3225
Polymers78,3225
Non-polymers00
Water00
1
A: HOV protease
D: HOV protease


Theoretical massNumber of molelcules
Total (without water)38,8972
Polymers38,8972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-15 kcal/mol
Surface area15570 Å2
MethodPISA
2
B: HOV protease
C: HOV protease


Theoretical massNumber of molelcules
Total (without water)38,8972
Polymers38,8972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area16020 Å2
MethodPISA
3
X: HOV protease fragment


  • defined by author&software
  • 529 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5291
Polymers5291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.757, 91.005, 141.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
HOV protease


Mass: 19448.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Strain: Hu/Houston/TCH186/2002/US / Plasmid: pET - 46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein/peptide HOV protease fragment


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Strain: Hu/Houston/TCH186/2002/US / Plasmid: pET - 46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium thiocyanate, 0.1 M Bis-Tris propane (pH 6.5), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2015
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18302 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.5
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.8 / CC1/2: 0.752 / Rpim(I) all: 0.487

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FYQ

2fyq


Resolution: 2.704→36.285 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.69
RfactorNum. reflection% reflection
Rfree0.2458 899 4.91 %
Rwork0.2066 --
obs0.2086 18302 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.704→36.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 0 0 5214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065341
X-RAY DIFFRACTIONf_angle_d1.037228
X-RAY DIFFRACTIONf_dihedral_angle_d7.7823142
X-RAY DIFFRACTIONf_chiral_restr0.056814
X-RAY DIFFRACTIONf_plane_restr0.006922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7036-2.87290.3325790.28611516X-RAY DIFFRACTION47
2.8729-3.09460.33531270.26122669X-RAY DIFFRACTION82
3.0946-3.40580.26971700.24273215X-RAY DIFFRACTION99
3.4058-3.89810.25521790.21653261X-RAY DIFFRACTION100
3.8981-4.90930.2191690.17023298X-RAY DIFFRACTION100
4.9093-36.28860.21671750.18743444X-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)
12.50470.24420.73562.07581.02790.79940.0305-0.2076-0.06210.27530.1292-0.72190.1051-0.0095-0.04910.11350.0069-0.05060.2217-0.06630.43114.86647.7874-26.4716
23.8475-1.90083.21992.4324-1.20493.3407-0.0546-0.5272-0.04770.37050.1028-0.2554-0.25720.07650.04140.4291-0.0149-0.22610.3284-0.10660.639117.093215.7253-19.9806
31.96360.1733-1.12970.96780.42240.9361-0.02690.04170.25720.0679-0.0233-0.25320.01850.26860.0780.23910.0461-0.08720.4254-0.03181.030426.28838.4526-29.8804
40.74560.2579-0.15451.3299-0.21340.56710.0806-0.09740.19420.00010.0395-0.0726-0.0199-0.04550.16740.0997-0.11280.09840.1858-0.02720.1998.868815.5145-37.4413
50.9648-1.1775-0.85431.76591.83432.658-0.0877-0.02070.06250.34920.03480.25810.1927-0.40250.19030.21680.06920.11280.3480.04880.2681-0.58917.9971-32.6419
60.75690.24260.5621.50610.79920.6871-0.080.16150.0314-0.11360.2101-0.0921-0.0805-0.11510.23260.044-0.03910.16360.22810.01750.2233.97215.0912-37.0627
72.60761.77112.56363.39711.50913.47260.0438-0.21380.01690.09730.06180.00360.0741-0.09120.07910.04350.0052-0.01390.20260.08490.1694-0.534817.7982-31.8411
82.4895-0.21460.13860.44040.17621.33990.04060.15890.11790.03630.0893-0.49050.00830.18560.25480.1441-0.0172-0.15910.2624-0.01720.821427.39-6.074-30.2615
93.45371.2841-0.26731.1724-0.05970.4548-0.08290.13840.1061-0.0894-0.0778-0.38890.10430.1583-0.13970.36850.01370.26390.3928-0.16691.082131.2611-11.1258-38.5886
100.34530.03060.05750.4904-0.04780.01630.01920.0844-0.1130.0719-0.1373-0.4784-0.07220.0794-0.18280.1010.0403-0.1750.33720.03860.616221.3816-14.5019-24.8757
110.7427-1.1160.05415.5018-2.07221.06690.11420.30630.2837-0.2063-0.0306-0.4093-0.32920.16370.09240.4708-0.06070.12260.4771-0.10020.339411.8954-16.4689-41.9958
121.85680.8397-0.28661.8699-0.77871.37790.2204-0.02460.26230.0206-0.20340.2653-0.2392-0.4362-0.010.1846-0.0008-0.0260.3439-0.11110.40584.9083-13.2448-27.3686
131.8965-0.56750.08371.2839-0.3930.84850.0166-0.0942-0.37420.14040.1563-0.39050.1241-0.00810.03970.01940.0721-0.15960.1744-0.00150.493916.5126-16.3309-29.112
143.3716-0.7385-0.49533.33851.52482.06270.0945-0.0330.05970.17520.0611-0.1046-0.28730.13540.12460.7337-0.0049-0.02830.3135-0.02690.13223.3008-2.6992-8.0894
151.0395-0.21510.19460.89370.5030.73080.0755-0.35980.35720.24150.06690.0059-0.24040.0273-0.11331.2795-0.01540.32160.5323-0.110.4376-3.6513-1.46692.1664
160.1901-0.17590.57033.76231.11452.4742-0.0489-0.1543-0.11470.6979-0.05530.2928-0.09890.02790.06360.54920.03160.03210.4393-0.0050.1621-1.1325-12.6811-11.9974
171.68591.1663-0.20331.0847-0.20921.86550.03-0.2642-0.20890.5482-0.2066-0.19820.24040.220.04370.75190.03560.0140.417-0.01270.37071.461-21.6574-6.3036
181.37550.032-0.74261.2469-0.01441.85260.0722-0.1456-0.07070.9904-0.1028-0.20150.32420.0831-0.01560.77360.0581-0.07020.33420.01170.20342.26-17.7563-10.0977
190.00330.0013-0.0007-0.0001-0.00130.00030.14090.24680.0281-0.0117-0.02410.0826-0.00180.0878-0.08691.17210.03640.09170.4731-0.1870.6269-23.2524-14.56150.223
202.1445-0.25180.42750.66860.35060.87550.04150.2157-0.4853-0.83410.0059-0.11730.5127-0.07030.06310.7149-0.03960.04230.1997-0.01350.22961.4955-11.4715-56.4041
210.8960.3308-0.05121.5595-0.63690.2695-0.00040.1842-0.5069-0.52640.12380.13070.1691-0.3056-0.08611.3527-0.1639-0.19120.44410.01740.5419-4.346-13.7772-62.0519
221.2325-0.2872-0.84712.79440.13610.6372-0.20830.16830.0615-0.87350.2836-0.0606-0.04390.0497-0.0850.4457-0.11540.01850.2176-0.00850.1924-1.68852.1178-53.5557
230.5995-0.0763-0.83681.177-0.69021.72510.10320.14690.0928-0.7478-0.0651-0.43060.01970.2805-0.10450.6352-0.06590.22620.2640.01490.32756.05779.2845-57.63
242.7546-0.7377-0.0691.76740.6082.78580.13630.1043-0.0573-0.5680.0098-0.0699-0.0798-0.0192-0.02330.7608-0.09890.04030.2419-0.01140.1257-0.49013.4169-56.8266
253.3986-2.38434.52542.0051-3.38746.30890.11290.07670.1368-0.19530.0097-0.3387-0.06250.1171-0.04860.5782-0.19410.05380.42280.00670.55996.0209-18.542-44.1995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 160 )
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 172 )
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 43 )
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 114 )
12X-RAY DIFFRACTION12chain 'B' and (resid 115 through 135 )
13X-RAY DIFFRACTION13chain 'B' and (resid 136 through 173 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 19 )
15X-RAY DIFFRACTION15chain 'C' and (resid 20 through 69 )
16X-RAY DIFFRACTION16chain 'C' and (resid 70 through 93 )
17X-RAY DIFFRACTION17chain 'C' and (resid 94 through 112 )
18X-RAY DIFFRACTION18chain 'C' and (resid 113 through 170 )
19X-RAY DIFFRACTION19chain 'C' and (resid 171 through 180 )
20X-RAY DIFFRACTION20chain 'D' and (resid -1 through 43 )
21X-RAY DIFFRACTION21chain 'D' and (resid 44 through 69 )
22X-RAY DIFFRACTION22chain 'D' and (resid 70 through 93 )
23X-RAY DIFFRACTION23chain 'D' and (resid 94 through 135 )
24X-RAY DIFFRACTION24chain 'D' and (resid 136 through 172 )
25X-RAY DIFFRACTION25chain 'X' and (resid 1 through 6 )

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