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- PDB-8ehn: PRRSV-1 PLP2 domain -

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Basic information

Entry
Database: PDB / ID: 8ehn
TitlePRRSV-1 PLP2 domain
Components(Papain-like protease 2) x 2
KeywordsVIRAL PROTEIN / PLP2 / DUB / deubiquitinating
Function / homology
Function and homology information


: / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / nucleotide binding / host cell nucleus ...: / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / nucleotide binding / host cell nucleus / proteolysis / membrane / metal ion binding / cytoplasm
Similarity search - Function
Arterivirus polyprotein, nsp2, non-essential region / Non-essential region of nsp2 of arterivirus polyprotein / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 ...Arterivirus polyprotein, nsp2, non-essential region / Non-essential region of nsp2 of arterivirus polyprotein / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBailey-Elkin, B.A. / Mark, B.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPAS-2020-00012 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-05682 Canada
CitationJournal: Plos Pathog. / Year: 2023
Title: Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis.
Authors: Bailey-Elkin, B.A. / Knaap, R.C.M. / De Silva, A. / Boekhoud, I.M. / Mous, S. / van Vught, N. / Khajehpour, M. / van den Born, E. / Kikkert, M. / Mark, B.L.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Papain-like protease 2
B: Papain-like protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2287
Polymers43,9202
Non-polymers3085
Water32418
1
A: Papain-like protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1785
Polymers21,9361
Non-polymers2434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Papain-like protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0492
Polymers21,9841
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.499, 102.347, 100.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Papain-like protease 2 / ORF1a


Mass: 21935.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Production host: Escherichia coli (E. coli) / References: UniProt: W0NX70
#2: Protein Papain-like protease 2 / ORF1a


Mass: 21983.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Production host: Escherichia coli (E. coli) / References: UniProt: W0NX70
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG 2000, 0.35M ammonium acetate, 0.1M HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→37.58 Å / Num. obs: 15677 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→8.91 Å / Num. unique obs: 1516 / CC1/2: 0.845

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 26.449 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25296 1565 10 %RANDOM
Rwork0.19998 ---
obs0.20534 14038 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.177 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å2-0 Å2
2--1.35 Å20 Å2
3----4.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 14 18 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0172387
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192185
X-RAY DIFFRACTIONr_angle_refined_deg1.441.8653279
X-RAY DIFFRACTIONr_angle_other_deg1.0362.5725049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82421.538117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28615341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0451518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_mcbond_it8.6315.741221
X-RAY DIFFRACTIONr_mcbond_other8.5655.7211217
X-RAY DIFFRACTIONr_mcangle_it10.7638.5991519
X-RAY DIFFRACTIONr_mcangle_other10.7628.61520
X-RAY DIFFRACTIONr_scbond_it9.2556.3231166
X-RAY DIFFRACTIONr_scbond_other9.2526.331167
X-RAY DIFFRACTIONr_scangle_other11.6389.2411761
X-RAY DIFFRACTIONr_long_range_B_refined14.49369.9282596
X-RAY DIFFRACTIONr_long_range_B_other14.50169.9692597
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 115 -
Rwork0.387 1038 -
obs--98.46 %
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)
13.05141.14341.287310.4512.56697.06220.0063-0.2152-0.2324-0.48210.07470.49320.0715-0.685-0.0810.1641-0.0323-0.05840.08240.03740.058440.57532.97753.755
23.20920.7666-2.59677.38543.946411.9402-0.19480.1966-0.0323-0.17970.4055-0.32340.5810.1741-0.21070.1833-0.01440.03560.0332-0.02190.026452.95438.68326.683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A417 - 566
2X-RAY DIFFRACTION2B416 - 570

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