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- PDB-4k7e: Crystal structure of Junin virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4k7e
TitleCrystal structure of Junin virus nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / alpha/beta/alpha sandwich / nucleoprotein
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesJunin virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y.J. / Li, L. / Liu, X. / Dong, S.S. / Wang, W.M. / Huo, T. / Rao, Z.H. / Yang, C.
CitationJournal: J.Gen.Virol. / Year: 2013
Title: Crystal structure of Junin virus nucleoprotein
Authors: Zhang, Y.J. / Li, L. / Liu, X. / Dong, S.S. / Wang, W.M. / Huo, T. / Guo, Y. / Rao, Z.H. / Yang, C.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,6681
Polymers26,6681
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleoprotein

A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,3352
Polymers53,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area1470 Å2
ΔGint-3 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.415, 78.472, 136.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 26667.738 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, residues 341-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Junin virus / Gene: N / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6IVU2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 2.2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→39.26 Å / Num. all: 11382 / Num. obs: 11370 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 32.11 Å2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 53.5 / Num. unique all: 11382 / % possible all: 99.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.256 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8133 / SU ML: 0.23 / σ(F): 0 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 544 4.78 %
Rwork0.1965 --
obs0.1979 11370 99.65 %
all-11382 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.851 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 41.8034 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--17.1704 Å20 Å2-0 Å2
2--24.6504 Å2-0 Å2
3----7.4801 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 78 1276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061229
X-RAY DIFFRACTIONf_angle_d1.0041668
X-RAY DIFFRACTIONf_chiral_restr0.064190
X-RAY DIFFRACTIONf_plane_restr0.005216
X-RAY DIFFRACTIONf_dihedral_angle_d14.837465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1997-2.4210.2621390.213326362775100
2.421-2.77120.30771370.217826772814100
2.7712-3.49110.24651350.204626922827100
3.4911-39.26230.17451330.18252821295499

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