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- PDB-8eho: PRRSV-1 PLP2 domain bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8eho
TitlePRRSV-1 PLP2 domain bound to ubiquitin
Components
  • Papain-like protease 2
  • Ubiquitin
KeywordsVIRAL PROTEIN / PLP2 / DUB / deubiquitinating
Function / homology
Function and homology information


: / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...: / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / host cell membrane / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN
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. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
3-AMINOPROPANE / NITRATE ION / Polyubiquitin-B / ORF1a
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 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

Downloads & links

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Assembly

Deposited unit
A: Papain-like protease 2
B: Ubiquitin
C: Papain-like protease 2
D: Ubiquitin
E: Papain-like protease 2
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,84120
Polymers91,7616
Non-polymers1,08014
Water3,099172
1
A: Papain-like protease 2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9587
Polymers30,5872
Non-polymers3715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Papain-like protease 2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9887
Polymers30,5872
Non-polymers4015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Papain-like protease 2
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8966
Polymers30,5872
Non-polymers3094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.686, 159.492, 147.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

21E-733-

HOH

31E-735-

HOH

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Papain-like protease 2 / ORF1a


Mass: 22067.125 Da / Num. of mol.: 3
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 Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 5 types, 186 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H9N
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Mg(NO3)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.85→45.84 Å / Num. obs: 24728 / % possible obs: 97.1 % / Redundancy: 4.7 % / CC1/2: 0.987 / Net I/σ(I): 7.9
Reflection shellResolution: 2.85→9.01 Å / Num. unique obs: 3640 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PDB-REDO5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ubq

1ubq


Resolution: 2.85→43.94 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.682 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 2.75 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24658 1156 4.7 %RANDOM
Rwork0.21247 ---
obs0.21408 23538 96.45 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å2-0 Å2-0 Å2
2--2.14 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 61 172 5810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0175766
X-RAY DIFFRACTIONr_bond_other_d0.0010.0195512
X-RAY DIFFRACTIONr_angle_refined_deg1.181.8787842
X-RAY DIFFRACTIONr_angle_other_deg0.9542.6412739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67422.366279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6241539
X-RAY DIFFRACTIONr_chiral_restr0.0610.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026407
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
X-RAY DIFFRACTIONr_mcbond_it0.9724.4852878
X-RAY DIFFRACTIONr_mcbond_other0.9734.4852876
X-RAY DIFFRACTIONr_mcangle_it1.7566.7213587
X-RAY DIFFRACTIONr_mcangle_other1.7566.7213587
X-RAY DIFFRACTIONr_scbond_it0.7724.5652888
X-RAY DIFFRACTIONr_scbond_other0.7724.5662886
X-RAY DIFFRACTIONr_scangle_other1.4176.8024253
X-RAY DIFFRACTIONr_long_range_B_refined4.21783.90322832
X-RAY DIFFRACTIONr_long_range_B_other4.20583.97922786
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 92 -
Rwork0.371 1731 -
obs--99.08 %

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