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- PDB-5da1: A Dimerization-Dependent Mechanism Drives PRRSV NSP11 Functions A... -

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Basic information

Entry
Database: PDB / ID: 5da1
TitleA Dimerization-Dependent Mechanism Drives PRRSV NSP11 Functions As a Beta Interferon Antagonist and Endoribonuclease
Componentsendoribonuclease
KeywordsHYDROLASE / Dimerization / NSP11 / Beta Interferon Antagonist / Endoribonuclease
Function / homology
Function and homology information


host cell membrane / RNA helicase activity / RNA helicase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 10, 1B domain, arterivirus / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / Arteriviridae zinc-binding (AV ZBD) domain profile. / Viral (Superfamily 1) RNA helicase / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain ...Nonstructural protein 10, 1B domain, arterivirus / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / Arteriviridae zinc-binding (AV ZBD) domain profile. / Viral (Superfamily 1) RNA helicase / 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. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Non-structural protein 8
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsShi, Y. / Peng, G.
Funding support China, 1items
OrganizationGrant numberCountry
Major State Basic Research Development Program2014CB542700 China
CitationJournal: To Be Published
Title: A Dimerization-Dependent Mechanism Drives PRRSV NSP11 Functions As a Beta Interferon Antagonist and Endoribonuclease
Authors: Shi, Y. / Peng, G.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endoribonuclease
B: endoribonuclease


Theoretical massNumber of molelcules
Total (without water)51,4432
Polymers51,4432
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.317, 77.317, 204.693
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 endoribonuclease


Mass: 25721.496 Da / Num. of mol.: 2 / Fragment: NSP11, UNP residues 1085-1307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Production host: Escherichia coli (E. coli) / References: UniProt: E3V2B6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.97 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium citrate tribasic dehydrate, PEG 3350 / PH range: 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 17000 / % possible obs: 100 % / Redundancy: 7.7 % / Net I/σ(I): 24.4
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4-1496refinement
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2819 855 5.05 %
Rwork0.2111 --
obs-16915 100 %
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 17 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013482
X-RAY DIFFRACTIONf_angle_d1.324745
LS refinement shellResolution: 2.7503→2.9226 Å
RfactorNum. reflection% reflection
Rfree0.3753 149 -
Rwork0.2707 2592 -
obs--100 %

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