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- PDB-4ium: Equine arteritis virus papain-like protease 2 (PLP2) covalently b... -

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Entry
Database: PDB / ID: 4ium
TitleEquine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
Components
  • Ubiquitin
  • papain-like protease 2
KeywordsHYDROLASE/PROTEIN BINDING / viral ovarian tumor domain (OTU) protease / deubiquitinase / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / 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 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Stabilization of p53 / Hh mutants are degraded by ERAD / Negative regulation of FGFR4 signaling / Activation of NF-kappaB in B cells / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / G2/M Checkpoints
Similarity search - Function
Cathepsin B; Chain A - #160 / 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 regulatory domain ...Cathepsin B; Chain A - #160 / 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 regulatory domain / RING/Ubox like zinc-binding domain / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / PRRSV nonstructural protein 11 N-terminal domain / 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 / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / 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. / Ubiquitin homologues / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Ubiquitin domain profile. / Ubiquitin-like domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Ubiquitin-like domain superfamily / 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. / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesEquine arteritis virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsBailey-Elkin, B.A. / James, T.W. / Mark, B.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells.
Authors: van Kasteren, P.B. / Bailey-Elkin, B.A. / James, T.W. / Ninaber, D.K. / Beugeling, C. / Khajehpour, M. / Snijder, E.J. / Mark, B.L. / Kikkert, M.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references / Structure summary
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0455
Polymers23,7952
Non-polymers2503
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.320, 62.040, 84.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein papain-like protease 2


Mass: 15234.333 Da / Num. of mol.: 1 / Fragment: UNP residues 261-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine arteritis virus / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ubiquitin


Mass: 8560.874 Da / Num. of mol.: 1 / Fragment: UNP residues 1-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM MES, pH 6.2, 18% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28243, 1.28289, 1.27347
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 29, 2011
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, uncoated, and Pd strips
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.282431
21.282891
31.273471
ReflectionResolution: 1.45→31.11 Å / Num. all: 36356 / Num. obs: 36344 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.5 / Redundancy: 8.7 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 7.1 / Num. unique all: 5029 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MxDCdata collection
PHENIX(phenix.autosol: 1.7.1_743))model building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→31.02 Å / SU ML: 0.26 / σ(F): 1.05 / Phase error: 17.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 1994 5.51 %RANDOM
Rwork0.1602 ---
obs0.1612 36216 99.55 %-
all-36344 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.83 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6234 Å20 Å2-0 Å2
2--5.8156 Å20 Å2
3----2.1922 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 13 260 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121606
X-RAY DIFFRACTIONf_angle_d1.4132182
X-RAY DIFFRACTIONf_dihedral_angle_d11.682608
X-RAY DIFFRACTIONf_chiral_restr0.077248
X-RAY DIFFRACTIONf_plane_restr0.009283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.31671340.27632289X-RAY DIFFRACTION95
1.4863-1.52640.2471400.21962391X-RAY DIFFRACTION99
1.5264-1.57140.20441390.18672400X-RAY DIFFRACTION100
1.5714-1.62210.21421430.16642438X-RAY DIFFRACTION100
1.6221-1.680.20141400.16132422X-RAY DIFFRACTION100
1.68-1.74730.18331420.15552451X-RAY DIFFRACTION100
1.7473-1.82680.18921420.15342431X-RAY DIFFRACTION100
1.8268-1.92310.16761410.15222426X-RAY DIFFRACTION100
1.9231-2.04360.16121420.15162427X-RAY DIFFRACTION100
2.0436-2.20130.18781430.14432451X-RAY DIFFRACTION100
2.2013-2.42280.14771440.14852480X-RAY DIFFRACTION100
2.4228-2.77320.16041440.14762471X-RAY DIFFRACTION100
2.7732-3.49320.16351470.15522520X-RAY DIFFRACTION100
3.4932-31.02710.18251530.16672625X-RAY DIFFRACTION100

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