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- PDB-5y4l: PRRSV nsp4 -

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Basic information

Entry
Database: PDB / ID: 5y4l
TitlePRRSV nsp4
ComponentsNon-structural proteinViral nonstructural protein
KeywordsVIRAL PROTEIN / 3C-like serine protease / apo-structure / virual protein / polyprotein processing
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 / host cell nucleus / proteolysis ...: / 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 / host cell nucleus / proteolysis / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Chymotrypsin-like serine protease; domain 3 / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / 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 ...Chymotrypsin-like serine protease; domain 3 / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / 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. / Herpes Virus-1 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Non-structural protein
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 Å
AuthorsShi, Y.J. / Gang, Y. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Vet. Microbiol. / Year: 2018
Title: Identification of two antiviral inhibitors targeting 3C-like serine/3C-like protease of porcine reproductive and respiratory syndrome virus and porcine epidemic diarrhea virus.
Authors: Shi, Y. / Lei, Y. / Ye, G. / Sun, L. / Fang, L. / Xiao, S. / Fu, Z.F. / Yin, P. / Song, Y. / Peng, G.
History
DepositionAug 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 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
B: Non-structural protein
A: Non-structural protein
C: Non-structural protein
D: Non-structural protein


Theoretical massNumber of molelcules
Total (without water)88,2364
Polymers88,2364
Non-polymers00
Water4,756264
1
B: Non-structural protein
C: Non-structural protein


Theoretical massNumber of molelcules
Total (without water)44,1182
Polymers44,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19 kcal/mol
Surface area17160 Å2
MethodPISA
2
A: Non-structural protein
D: Non-structural protein


Theoretical massNumber of molelcules
Total (without water)44,1182
Polymers44,1182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-18 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.681, 86.117, 142.955
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
Non-structural protein / Viral nonstructural protein


Mass: 22058.947 Da / Num. of mol.: 4 / Fragment: UNP residues 1780-1983
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Gene: ORF1a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1E8J1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 48853 / % possible obs: 92.4 % / Redundancy: 5.5 % / Net I/σ(I): 11.14

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.198→37.544 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.46
RfactorNum. reflection% reflection
Rfree0.2522 2000 4.13 %
Rwork0.2129 --
obs0.2145 48378 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.198→37.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 0 264 6048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095909
X-RAY DIFFRACTIONf_angle_d1.1698014
X-RAY DIFFRACTIONf_dihedral_angle_d13.3972054
X-RAY DIFFRACTIONf_chiral_restr0.046898
X-RAY DIFFRACTIONf_plane_restr0.0061054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1978-2.25270.31521350.26423133X-RAY DIFFRACTION95
2.2527-2.31360.33791410.26033285X-RAY DIFFRACTION99
2.3136-2.38170.2731420.25023269X-RAY DIFFRACTION99
2.3817-2.45860.32311410.24553285X-RAY DIFFRACTION99
2.4586-2.54640.3311410.24213278X-RAY DIFFRACTION99
2.5464-2.64840.27551410.24413260X-RAY DIFFRACTION99
2.6484-2.76890.28081440.23513317X-RAY DIFFRACTION100
2.7689-2.91480.27051420.23573307X-RAY DIFFRACTION100
2.9148-3.09730.26511440.22583325X-RAY DIFFRACTION100
3.0973-3.33630.27421440.22843339X-RAY DIFFRACTION99
3.3363-3.67180.25911440.21363333X-RAY DIFFRACTION99
3.6718-4.20250.21481430.19913341X-RAY DIFFRACTION99
4.2025-5.29240.19661450.17393375X-RAY DIFFRACTION99
5.2924-37.54980.23621530.19053531X-RAY DIFFRACTION99

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