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- PDB-7mc9: X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA -

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Basic information

Entry
Database: PDB / ID: 7mc9
TitleX-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA
Components
  • 3C-like proteinase
  • Ubiquitin
KeywordsHYDROLASE / coronavirus / PLP / PLP2 / papain-like protease / PEDV / UB-PA / complex / cysteine-protease
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 / host cell membrane ...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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / viral genome replication / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / regulation of mitochondrial membrane potential / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / positive regulation of protein ubiquitination / 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 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Regulation of signaling by CBL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import
Similarity search - Function
Papain-like viral protease, thumb domain / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / Helicase, Ruva Protein; domain 3 ...Papain-like viral protease, thumb domain / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Ubiquitin family / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Ubiquitin homologues / Ubiquitin domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Ubiquitin-like domain / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus
Similarity search - Domain/homology
prop-2-en-1-amine / ORF1ab polyprotein / Polyubiquitin-B
Similarity search - Component
Biological speciesPorcine epidemic diarrhea virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsDurie, I.A. / Dzimianski, J.V. / Daczkowski, C.M. / Pegan, S.D.
Funding support United States, 3items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)58-5030-5034 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
CitationJournal: Acta Cryst. D / Year: 2021
Title: Structural insights into the interaction of papain-like protease 2 from the alphacoronavirus porcine epidemic diarrhea virus and ubiquitin
Authors: Durie, I.A. / Dzimianski, J.V. / Daczkowski, C.M. / McGuire, J. / Faaberg, K. / Pegan, S.D.
History
DepositionApr 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: Ubiquitin
C: 3C-like proteinase
D: Ubiquitin
E: 3C-like proteinase
F: Ubiquitin
G: 3C-like proteinase
H: Ubiquitin
I: 3C-like proteinase
J: Ubiquitin
K: 3C-like proteinase
L: Ubiquitin
M: 3C-like proteinase
N: Ubiquitin
O: 3C-like proteinase
P: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,02938
Polymers274,65716
Non-polymers1,37222
Water1629
1
A: 3C-like proteinase
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5856
Polymers34,3322
Non-polymers2534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3C-like proteinase
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4554
Polymers34,3322
Non-polymers1232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 3C-like proteinase
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5856
Polymers34,3322
Non-polymers2534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 3C-like proteinase
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5205
Polymers34,3322
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: 3C-like proteinase
J: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4554
Polymers34,3322
Non-polymers1232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: 3C-like proteinase
L: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4554
Polymers34,3322
Non-polymers1232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: 3C-like proteinase
N: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5205
Polymers34,3322
Non-polymers1883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: 3C-like proteinase
P: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4554
Polymers34,3322
Non-polymers1232
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.138, 136.873, 193.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3C-like proteinase / Exoribonuclease / Growth factor-like peptide / Helicase / M-PRO / NendoU / Non-structural protein 1 ...Exoribonuclease / Growth factor-like peptide / Helicase / M-PRO / NendoU / Non-structural protein 1 / Non-structural protein 10 / Non-structural protein 2 / Non-structural protein 3 / Non-structural protein 4 / Non-structural protein 6 / Non-structural protein 7 / Non-structural protein 8 / Non-structural protein 9 / ORF1ab polyprotein / PL1-PRO/PL2-PRO / PLP1/PLP2 / Papain-like proteinases 1/2 / Peptide HD2 / Putative 2'-O-methyl transferase / RNA-directed RNA polymerase / Replicase polyprotein 1ab / Uridylate-specific endoribonuclease / nsp12 / nsp15 / nsp16 / nsp5 / p12 / p195 / p23 / p34 / p5 / p87 / p9


Mass: 25812.311 Da / Num. of mol.: 8 / Fragment: Peptidase C16 domain, residues 1690-1922
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Gene: ORF1ab
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0S3MQV7, ubiquitinyl hydrolase 1, DNA helicase, RNA helicase
#2: Protein
Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 8
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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.30M MgCl2, 0.1M Tris, and 16% PEG 4k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.099→49.069 Å / Num. obs: 46738 / % possible obs: 97.21 % / Redundancy: 6.1 % / CC1/2: 0.972 / CC star: 0.993 / Net I/σ(I): 4.66
Reflection shellResolution: 3.099→3.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1 / Num. unique obs: 4185 / CC1/2: 0.614 / CC star: 0.872 / Rrim(I) all: 0.936 / Χ2: 0.345 / % possible all: 88.58

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NOZ

6noz


Resolution: 3.099→49.069 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 2350 5.03 %
Rwork0.2003 44383 -
obs0.2032 46733 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.34 Å2 / Biso mean: 53.9069 Å2 / Biso min: 13.03 Å2
Refinement stepCycle: final / Resolution: 3.099→49.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 46 9 19153
Biso mean--63.94 34.19 -
Num. residues----2465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.099-3.1620.36741310.283231688
3.162-3.23070.28741230.2665237390
3.2307-3.30590.34031200.2589242192
3.3059-3.38850.33311260.2449252894
3.3885-3.48010.32691410.243249696
3.4801-3.58250.30251130.2296263597
3.5825-3.69810.29621320.2319260098
3.6981-3.83020.29561480.2328264399
3.8302-3.98350.29141370.21932651100
3.9835-4.16470.2911580.19922640100
4.1647-4.38420.22531570.17372658100
4.3842-4.65860.23311460.16772694100
4.6586-5.0180.22751270.15632696100
5.018-5.52240.19451250.15972724100
5.5224-6.320.22911570.19192699100
6.32-7.95710.25991370.19612770100
7.9571-49.0690.19091720.1693283999

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