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- PDB-3mtv: The Crystal Structure of the PRRSV Nonstructural Protein Nsp1 -

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Basic information

Entry
Database: PDB / ID: 3mtv
TitleThe Crystal Structure of the PRRSV Nonstructural Protein Nsp1
ComponentsPapain-like cysteine protease
KeywordsHYDROLASE / PRRSV / nsp1 / nuclease / papain-like cysteine protease
Function / homology
Function and homology information


host cell membrane / helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Arterivirus nps1beta, nuclease domain / Arterivirus papain-like cysteine protease beta domain / 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 nps1beta, nuclease domain / Arterivirus papain-like cysteine protease beta domain / 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. / Transcriptional Co-activator pc4; Chain A / Cathepsin B; Chain A / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 6
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsXue, F. / Sun, Y.N. / Yan, L.M. / Zhao, C. / Lou, Z.Y. / Rao, Z.H.
CitationJournal: J.Virol. / Year: 2010
Title: The crystal structure of porcine reproductive and respiratory syndrome virus nonstructural protein Nsp1beta reveals a novel metal-dependent nuclease
Authors: Xue, F. / Sun, Y.N. / Yan, L.M. / Zhao, C. / Chen, J. / Bartlam, M. / Li, X.M. / Lou, Z.Y. / Rao, Z.H.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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
A: Papain-like cysteine protease


Theoretical massNumber of molelcules
Total (without water)23,0931
Polymers23,0931
Non-polymers00
Water36020
1
A: Papain-like cysteine protease

A: Papain-like cysteine protease


Theoretical massNumber of molelcules
Total (without water)46,1872
Polymers46,1872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2470 Å2
ΔGint-15 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.895, 100.895, 81.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Papain-like cysteine protease / nsp1b


Mass: 23093.434 Da / Num. of mol.: 1 / Fragment: UNP residues 181-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B2ZAB4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM HEPES (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-17A20.9798, 0.9795, 0.960
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 15, 2009
ADSC QUANTUM 2702CCDMar 15, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97981
30.97951
40.961
ReflectionResolution: 2.8→31.91 Å / Num. all: 12120 / Num. obs: 12021 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Biso Wilson estimate: 74.95 Å2 / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.8→2.8 Å / Redundancy: 11.2 % / Num. unique all: 1189 / Rsym value: 0.421 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→31.906 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 0.22 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 506 4.77 %random
Rwork0.2005 10098 --
obs0.2035 10604 97.72 %-
all-12120 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.127 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso max: 161.46 Å2 / Biso mean: 68.325 Å2 / Biso min: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1-3.473 Å20 Å2-0 Å2
2--3.473 Å20 Å2
3----6.9461 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 0 20 1652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0381683
X-RAY DIFFRACTIONf_angle_d3.4262285
X-RAY DIFFRACTIONf_dihedral_angle_d21.951625
X-RAY DIFFRACTIONf_chiral_restr0.188236
X-RAY DIFFRACTIONf_plane_restr0.018296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08160.35721110.26682362X-RAY DIFFRACTION93
3.0816-3.5270.30361220.2282492X-RAY DIFFRACTION98
3.527-4.44180.26121350.18042549X-RAY DIFFRACTION100
4.4418-31.90790.21791380.18142695X-RAY DIFFRACTION100

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