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- PDB-4x2v: Crystal structure of the Murine Norovirus NS6 protease (inactive ... -

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Basic information

Entry
Database: PDB / ID: 4x2v
TitleCrystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residue P1 prime of NS7
Components(NS6 Protease) x 3
KeywordsHYDROLASE / Murine norovirus Protease
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / NTPase / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFernandes, H. / Leen, E.N. / Curry, S.
Citation
Journal: Peerj / Year: 2015
Title: Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions.
Authors: Fernandes, H. / Leen, E.N. / Cromwell, H. / Pfeil, M.P. / Curry, S.
#1: Journal: PLoS ONE / Year: 2012
Title: Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation.
Authors: Leen, E.N. / Baeza, G. / Curry, S.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS6 Protease
B: NS6 Protease
C: NS6 Protease
D: NS6 Protease
E: NS6 Protease
F: NS6 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7487
Polymers78,6796
Non-polymers691
Water1,58588
1
A: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)19,3681
Polymers19,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)19,3681
Polymers19,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)19,3681
Polymers19,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NS6 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4372
Polymers19,3681
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NS6 Protease


  • defined by author
  • 593 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5931
Polymers5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NS6 Protease


  • defined by author
  • 614 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6141
Polymers6141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.640, 111.860, 81.290
Angle α, β, γ (deg.)90.000, 119.240, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLYAA1 - 1732 - 174
21ALAALAGLYGLYBB1 - 1732 - 174
12VALVALGLYGLYAA3 - 1734 - 174
22VALVALGLYGLYCC3 - 1734 - 174
13VALVALHISHISAA3 - 1724 - 173
23VALVALHISHISDD3 - 1724 - 173
14VALVALGLYGLYBB3 - 1734 - 174
24VALVALGLYGLYCC3 - 1734 - 174
15VALVALHISHISBB3 - 1724 - 173
25VALVALHISHISDD3 - 1724 - 173
16VALVALHISHISCC3 - 1724 - 173
26VALVALHISHISDD3 - 1724 - 173

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NS6 Protease


Mass: 19368.127 Da / Num. of mol.: 4 / Fragment: UNP residues 995-1178 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: A0FJD7, UniProt: Q80J95*PLUS
#2: Protein/peptide NS6 Protease


Mass: 592.641 Da / Num. of mol.: 1 / Fragment: UNP residues 1174-1178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q80J95
#3: Protein/peptide NS6 Protease


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Strain: CW1 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 10% (v/v) poly-ethylene glycol (PEG) 10000, 20% (v/v) ethylene glycol, 0.1 M MES/Imidazole pH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→70.93 Å / Num. obs: 34593 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ASH

4ash


Resolution: 2.3→70.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 26.908 / SU ML: 0.313 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.708 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2781 860 3.3 %Random selection
Rwork0.2301 25132 --
obs0.2317 25992 75.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 224.6 Å2 / Biso mean: 77.327 Å2 / Biso min: 19.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å2-0 Å21.2 Å2
2---0.79 Å2-0 Å2
3---2.21 Å2
Refinement stepCycle: final / Resolution: 2.3→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5247 0 5 88 5340
Biso mean--36.73 42.02 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195393
X-RAY DIFFRACTIONr_bond_other_d0.0070.025195
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9317330
X-RAY DIFFRACTIONr_angle_other_deg1.329311911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7935712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25422.872188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07315816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4151526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216154
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021254
X-RAY DIFFRACTIONr_mcbond_it1.2772.0552854
X-RAY DIFFRACTIONr_mcbond_other1.2772.0542853
X-RAY DIFFRACTIONr_mcangle_it2.1543.0713558
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89140.12
12B89140.12
21A89730.1
22C89730.1
31A89300.12
32D89300.12
41B90930.12
42C90930.12
51B89530.11
52D89530.11
61C88070.12
62D88070.12
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 4 -
Rwork0.297 215 -
all-219 -
obs--8.7 %
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)
17.1732-0.62173.68734.3188-0.45697.77850.20960.05350.24210.0911-0.55080.11250.165-0.9240.34110.3377-0.01790.05340.2856-0.0880.0498-48.5766.48182.491
231.2433-25.49333.26690.435133.129418.8236-2.4823-1.30822.1670.05682.0716-1.125-1.22430.07090.41081.06920.0003-0.07121.50740.1770.8328-51.88120.19998.229
310.73681.21420.837911.6374-0.743610.32010.1419-0.95830.58340.5789-0.6726-0.2856-0.1762-0.31840.53070.461-0.04160.01290.1831-0.0660.0703-41.167.77693.844
45.27840.4689-1.11943.92450.26797.8749-0.0080.74720.2485-0.0807-0.2467-0.85720.7141.97880.25470.42390.27710.03010.82940.23220.2381-14.562-2.92281.232
54.0601-3.2099-2.566666.996822.39218.8225-0.53320.225-1.25870.42780.4234-0.80650.64930.67990.10980.78690.1332-0.09880.74980.01090.6673-16.118-15.97697.09
64.6537-5.38943.86896.9119-3.36656.17610.05530.33050.42280.1998-0.4409-0.62590.59670.83390.38560.89950.0647-0.01790.40740.19620.1297-20.143-6.37894.577
73.2505-0.85270.17848.9621-3.3396.3684-0.317-0.4639-0.51811.3990.16480.81630.4938-0.46290.15220.92750.06320.19310.12450.03180.1771-33.909-20.626124.961
84.6677-2.03280.3559.45730.008611.6146-0.32610.3316-0.01630.3937-0.0156-0.2815-0.27320.4250.34160.52610.0237-0.03890.08860.01590.0247-29.974-7.736113.458
910.93684.5279-3.152614.9421-0.52438.2726-0.24050.4157-0.29330.054-0.0545-0.38330.41480.51360.2950.50520.0494-0.05350.1180.020.0326-28.825-12.635112.29
104.3801-0.39370.07427.90943.732511.8577-0.7541-1.04660.69451.187-0.17230.0525-2.4128-0.82870.92641.9330.4376-0.46210.4241-0.26680.2061-38.1817.73128.442
1193.2858-26.8154-12.958316.67773.21321.834-0.42290.181-0.63520.65150.47062.30250.115-0.0704-0.04781.77080.0377-0.31271.3017-0.16750.7094-50.30219.358112.459
1210.6909-3.5229-0.388913.31251.935414.9604-0.50990.01380.22630.1839-0.36190.7111-0.9713-1.12450.87180.93550.2684-0.16350.2093-0.1250.1145-40.18210.377116.611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2A104 - 115
3X-RAY DIFFRACTION3A116 - 174
4X-RAY DIFFRACTION4B0 - 101
5X-RAY DIFFRACTION5B102 - 115
6X-RAY DIFFRACTION6B116 - 184
7X-RAY DIFFRACTION7C3 - 79
8X-RAY DIFFRACTION8C80 - 150
9X-RAY DIFFRACTION9C151 - 174
10X-RAY DIFFRACTION10D3 - 101
11X-RAY DIFFRACTION11D102 - 113
12X-RAY DIFFRACTION12D114 - 173

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