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- PDB-5eyi: Structure of PRRSV apo-NSP11 at 2.16A -

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Basic information

Entry
Database: PDB / ID: 5eyi
TitleStructure of PRRSV apo-NSP11 at 2.16A
ComponentsNon-structural protein 11
KeywordsHYDROLASE / Non-structural protein 11 / Nsp11 / Beta Interferon Antagonist / Endoribonuclease
Function / homology
Function and homology information


: / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 ...: / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 10, 1B domain, arterivirus / 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 / Nonstructural protein 10, zinc-binding domain, arterivirus ...Nonstructural protein 10, 1B domain, arterivirus / 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 / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / 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 / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesPRRSV 16244B (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsZhang, M.F. / Chen, Z.
CitationJournal: J. Virol. / Year: 2017
Title: Structural Biology of the Arterivirus nsp11 Endoribonucleases.
Authors: Zhang, M. / Li, X. / Deng, Z. / Chen, Z. / Liu, Y. / Gao, Y. / Wu, W. / Chen, Z.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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: Non-structural protein 11
B: Non-structural protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1775
Polymers49,9252
Non-polymers2523
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-14 kcal/mol
Surface area20730 Å2
Unit cell
Length a, b, c (Å)75.299, 75.299, 199.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-346-

HOH

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Components

#1: Protein Non-structural protein 11


Mass: 24962.703 Da / Num. of mol.: 2 / Mutation: K173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PRRSV 16244B (virus) / Strain: 16244B / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YN02
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. all: 31952 / Num. obs: 31822 / % possible obs: 99.6 % / Redundancy: 7.7 % / Net I/σ(I): 19
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.102 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21028 1607 5.1 %RANDOM
Rwork0.18441 ---
obs0.18578 29712 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 14 440 3823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193477
X-RAY DIFFRACTIONr_bond_other_d0.0020.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9684735
X-RAY DIFFRACTIONr_angle_other_deg0.90137578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.83622.632133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43515545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4271519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2452.791728
X-RAY DIFFRACTIONr_mcbond_other1.2452.7891727
X-RAY DIFFRACTIONr_mcangle_it2.1164.1732153
X-RAY DIFFRACTIONr_mcangle_other2.1154.1742154
X-RAY DIFFRACTIONr_scbond_it1.5382.9981749
X-RAY DIFFRACTIONr_scbond_other1.5372.9991750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.64.3992582
X-RAY DIFFRACTIONr_long_range_B_refined5.33523.5064046
X-RAY DIFFRACTIONr_long_range_B_other5.16423.2243969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.156→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 99 -
Rwork0.262 1863 -
obs--84.97 %

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