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- PDB-1mbm: NSP4 proteinase from Equine Arteritis Virus -

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Basic information

Entry
Database: PDB / ID: 1mbm
TitleNSP4 proteinase from Equine Arteritis Virus
Componentschymotrypsin-like serine protease
KeywordsTRANSFERASE / serine proteinase / chymotrypsin-like proteinase / collapsed oxyanion hole
Function / homology
Function and homology information


serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Chymotrypsin-like serine protease; domain 3 / Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab ...Chymotrypsin-like serine protease; domain 3 / Protein of unknown function DUF3756 / Equine arteritis virus, non-structural protein 1 / Nsp2, transmembrane domain / Replicase polyprotein 1ab / Nidovirus helicase, RING/Ubox like zinc-binding domain / Protein of unknown function (DUF3756) / Papain-like auto-proteinase / Nsp2, transmembrane domain / Replicase polyprotein 1ab / RING/Ubox like zinc-binding domain / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / Arteriviridae zinc-binding (AV ZBD) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Viral (Superfamily 1) RNA helicase / Herpes Virus-1 / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesEquine arteritis virus
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsBarrette-Ng, I.H. / Ng, K.K.-S. / Mark, B.L. / van Aken, D. / Cherney, M.M. / Garen, C. / Kolodenko, Y. / Gorbalenya, A.E. / Snijder, E.J. / James, M.N.G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of Arterivirus nsp4: the smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole
Authors: Barrette-Ng, I.H. / Ng, K.K.-S. / Mark, B.L. / van Aken, D. / Cherney, M.M. / Garen, C. / Kolodenko, Y. / Gorbalenya, A.E. / Snijder, E.J. / James, M.N.G.
History
DepositionAug 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: chymotrypsin-like serine protease
B: chymotrypsin-like serine protease
C: chymotrypsin-like serine protease
D: chymotrypsin-like serine protease


Theoretical massNumber of molelcules
Total (without water)81,5114
Polymers81,5114
Non-polymers00
Water7,206400
1
A: chymotrypsin-like serine protease


Theoretical massNumber of molelcules
Total (without water)20,3781
Polymers20,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chymotrypsin-like serine protease


Theoretical massNumber of molelcules
Total (without water)20,3781
Polymers20,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: chymotrypsin-like serine protease


Theoretical massNumber of molelcules
Total (without water)20,3781
Polymers20,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: chymotrypsin-like serine protease


Theoretical massNumber of molelcules
Total (without water)20,3781
Polymers20,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.612, 60.326, 62.637
Angle α, β, γ (deg.)74.08, 63.30, 66.18
Int Tables number1
Space group name H-MP1
Detailsprotein is a monomer in solution

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Components

#1: Protein
chymotrypsin-like serine protease / NSP4 Proteinase


Mass: 20377.699 Da / Num. of mol.: 4 / Fragment: Residues 1071-1268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus / Genus: Arterivirus / Gene: NSP4 / Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli)
References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PEG 8000, sodium cirate, ethylene glycol, sodium malonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 105K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
223 %(w/v)PEG2000 MME1reservoir
3100 mMTris1reservoirpH8.5
4100 %(w/v)ethylene glycol1reservoir
50.2 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 20, 2001 / Details: Osmic confocal mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 43171 / Num. obs: 43171 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 6.1 / Num. unique all: 4151 / Rsym value: 0.179 / % possible all: 91.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 16.2 Å / Num. measured all: 169296 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 91.5 % / Num. unique obs: 4151 / Num. measured obs: 15362 / Rmerge(I) obs: 0.179

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MIR / Resolution: 2→16.22 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.894 / SU ML: 135.62 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.247 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS tensors were refined for each of the three domains in each of the four copies of the asymmetric unit
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2161 5 %RANDOM
Rwork0.20441 ---
all0.208 43166 --
obs0.20726 43166 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.565 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.89 Å20.28 Å2
2--2.07 Å20.35 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2→16.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 0 400 5997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215709
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9437805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6493772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34315926
X-RAY DIFFRACTIONr_chiral_restr0.0830.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024270
X-RAY DIFFRACTIONr_nbd_refined0.1850.32518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.5741
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.378
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.537
X-RAY DIFFRACTIONr_mcbond_it1.85423826
X-RAY DIFFRACTIONr_mcangle_it3.04446155
X-RAY DIFFRACTIONr_scbond_it4.05141883
X-RAY DIFFRACTIONr_scangle_it5.6961650
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 145 -
Rwork0.222 2851 -
obs-2851 91 %
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)
12.67110.6167-0.61253.178-0.96693.47270.1073-0.1141-0.12180.2591-0.2744-0.3175-0.22330.51450.16720.0913-0.0381-0.03310.03970.05760.135636.058729.160444.3244
22.85361.0584-0.39271.3843-0.32562.5640.0537-0.03940.070.1732-0.0550.0136-0.1783-0.24640.00140.10570.01640.02170.00650.02360.107819.429726.396147.4738
31.55190.1295-1.425-0.8305-0.46672.04410.11480.01920.37010.1328-0.00120.0126-0.4004-0.2942-0.11360.20180.00660.02620.14640.03410.15445.137224.465654.8345
43.418-0.3070.34351.13080.85883.1108-0.10860.0356-0.1433-0.06560.05160.2273-0.0107-0.23920.0570.27260.0636-0.01960.2405-0.02270.192347.681324.487926.5635
54.998-0.16960.88182.05763.35719.25120.03870.3263-0.003-0.383-0.1806-0.0495-0.8805-0.60140.14190.18040.07050.03270.1360.00870.083364.521421.653324.3603
61.5068-1.1556-2.36660.15663.98259.92830.13810.08950.3047-0.20190.04330.0614-0.55870.0484-0.18140.15230.00740.05570.13150.0130.16780.316516.246118.9832
74.77730.8688-0.58193.38950.1912.33210.2055-0.47460.41620.2735-0.24680.50470.0656-0.14870.04120.0818-0.05550.04730.0641-0.06590.175743.997451.652139.271
86.2311.7351.03142.24851.17023.52910.1866-0.78540.24580.3348-0.0937-0.05790.00920.1645-0.09290.0945-0.0082-0.00930.127-0.06060.106760.712755.205341.1405
93.5592.09964.66693.37485.164512.0905-0.07-0.0501-0.34060.17270.1133-0.04410.268-0.0612-0.04330.084-0.007-0.01890.0784-0.0160.161176.694560.349946.4569
103.599-0.979-0.13252.25090.29031.95260.07130.2073-0.0057-0.1187-0.0788-0.32330.06260.47170.00750.15050.0458-0.01160.2859-0.01380.156732.106946.522321.9151
114.7083-1.0965-0.7271.11760.39276.73320.15210.2716-0.048-0.08660.07980.08780.4860.2591-0.23190.09770.0041-0.0560.06020.00750.085415.580149.825618.237
120.96920.39981.1121.5241-1.61179.4380.14930.0444-0.3758-0.1486-0.0382-0.02080.657-0.2453-0.11110.1167-0.0104-0.02820.1040.05480.1749-0.110753.46411.2126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 841 - 78
2X-RAY DIFFRACTION2AA85 - 15679 - 150
3X-RAY DIFFRACTION3AA157 - 203151 - 197
4X-RAY DIFFRACTION4BB7 - 841 - 78
5X-RAY DIFFRACTION5BB85 - 15679 - 150
6X-RAY DIFFRACTION6BB157 - 198151 - 192
7X-RAY DIFFRACTION7CC7 - 841 - 78
8X-RAY DIFFRACTION8CC85 - 15679 - 150
9X-RAY DIFFRACTION9CC157 - 197151 - 191
10X-RAY DIFFRACTION10DD9 - 843 - 78
11X-RAY DIFFRACTION11DD85 - 15679 - 150
12X-RAY DIFFRACTION12DD157 - 197151 - 191
Refinement
*PLUS
Lowest resolution: 16.2 Å / % reflection Rfree: 10 % / Rfactor all: 0.208 / Rfactor obs: 0.20726 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.271
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.222

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