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- PDB-4x2w: Crystal structure of the Murine Norovirus NS6 protease (inactive ... -

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Basic information

Entry
Database: PDB / ID: 4x2w
TitleCrystal structure of the Murine Norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residues P1 prime - P2 prime of NS7
ComponentsNS6 Protease
KeywordsHYDROLASE / Murine norovirus Protease
Function / homology
Function and homology information


calicivirin / host cell mitochondrion / host cell endosome membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity ...calicivirin / host cell mitochondrion / host cell endosome membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
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
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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Assembly

Deposited unit
A: NS6 Protease
B: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)37,5612
Polymers37,5612
Non-polymers00
Water00
1
A: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,7811
Polymers18,7811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS6 Protease


Theoretical massNumber of molelcules
Total (without water)18,7811
Polymers18,7811
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.940, 135.940, 82.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 4 - 181 / Label seq-ID: 2 - 179

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein NS6 Protease


Mass: 18780.504 Da / Num. of mol.: 2 / Fragment: UNP residues 997-1175 / Mutation: C139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q80J95

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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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% (v/v) PEG 3350, 0.1 M glycine, 0.1 M Na-citrate pH 7.0

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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 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→117.85 Å / Num. obs: 8555 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.9
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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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: 2.7→117.85 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.863 / SU B: 67.36 / SU ML: 0.534 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3025 469 4.9 %Random selection
Rwork0.2536 9071 --
obs0.256 8555 74.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.26 Å2 / Biso mean: 87.171 Å2 / Biso min: 42.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20.49 Å20 Å2
2--0.99 Å20 Å2
3----3.21 Å2
Refinement stepCycle: final / Resolution: 2.7→117.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 0 2562
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192622
X-RAY DIFFRACTIONr_bond_other_d0.0050.022520
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9373565
X-RAY DIFFRACTIONr_angle_other_deg1.12935785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.675342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.31722.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73115400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212958
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02594
X-RAY DIFFRACTIONr_mcbond_it1.1782.4651379
X-RAY DIFFRACTIONr_mcbond_other1.1782.4641378
X-RAY DIFFRACTIONr_mcangle_it2.1663.6881718
Refine LS restraints NCS

Ens-ID: 1 / Number: 8802 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 11 -
Rwork0.395 139 -
all-150 -
obs--16.03 %
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)
16.41181.3608-0.67245.8139-0.14967.8662-0.3530.1345-0.01390.18250.1922-0.26960.5666-0.39470.16080.6323-0.1315-0.08490.0463-0.0090.3524-9.292695.097387.4157
24.1189-0.49092.04577.6535-0.19247.97470.08410.4669-0.01650.03550.08260.7932-0.5622-1.0079-0.16670.8080.21410.03570.28980.06640.6194-22.0722114.9208107.103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 181
2X-RAY DIFFRACTION2B4 - 181

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