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- PDB-4j1j: Leanyer orthobunyavirus nucleoprotein-ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 4j1j
TitleLeanyer orthobunyavirus nucleoprotein-ssDNA complex
Components
  • DNA (5'-D(P*AP*CP*CP*AP*AP*AP*CP*AP*AP*CP*CP*CP*AP*CP*CP*CP*A)-3')
  • NucleocapsidCapsid
KeywordsVIRAL PROTEIN/DNA / PROTEIN-DNA COMPLEX / nucleic acids binding protein / nucleocapsid protein / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Bunyavirus nucleocapsid (N) protein, C-terminal domain / Poly(ADP-ribose) Polymerase; domain 1 - #20 / Bunyavirus nucleocapsid (N) protein / Bunyavirus nucleocapsid (N) , C-terminal domain / Bunyavirus nucleocapsid (N) , N-terminal domain / Bunyavirus nucleocapsid (N) protein / Poly(ADP-ribose) Polymerase; domain 1 / Cyclin A; domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesLeanyer virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNiu, F. / Shaw, N. / Wang, Y. / Jiao, L. / Ding, W. / Li, X. / Zhu, P. / Upur, H. / Ouyang, S. / Cheng, G. / Liu, Z.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation.
Authors: Niu, F. / Shaw, N. / Wang, Y.E. / Jiao, L. / Ding, W. / Li, X. / Zhu, P. / Upur, H. / Ouyang, S. / Cheng, G. / Liu, Z.J.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Nov 5, 2014Group: Structure summary
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: Nucleocapsid
A: Nucleocapsid
B: Nucleocapsid
C: Nucleocapsid
H: DNA (5'-D(P*AP*CP*CP*AP*AP*AP*CP*AP*AP*CP*CP*CP*AP*CP*CP*CP*A)-3')
I: DNA (5'-D(P*AP*CP*CP*AP*AP*AP*CP*AP*AP*CP*CP*CP*AP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)115,3086
Polymers115,3086
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.403, 73.199, 77.905
Angle α, β, γ (deg.)70.89, 82.54, 73.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleocapsid / Capsid


Mass: 26295.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leanyer virus / Production host: Escherichia coli (E. coli) / References: UniProt: F2WAD7
#2: DNA chain DNA (5'-D(P*AP*CP*CP*AP*AP*AP*CP*AP*AP*CP*CP*CP*AP*CP*CP*CP*A)-3')


Mass: 5063.333 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence has been designed and the ssDNA was synthesised.
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.4 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl (pH 7.5) and 20% w/v PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.65→43.33 Å / Num. all: 28964 / Num. obs: 27429 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.68→2.78 Å / % possible all: 84

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J1G

4j1g


Resolution: 2.65→43.33 Å / SU ML: 0.32 / σ(F): 1.96 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1996 7.28 %RANDOM
Rwork0.2227 ---
all0.2241 28964 --
obs0.2236 27429 93.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7329 678 0 68 8075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078259
X-RAY DIFFRACTIONf_angle_d1.28211297
X-RAY DIFFRACTIONf_dihedral_angle_d17.3523071
X-RAY DIFFRACTIONf_chiral_restr0.0781244
X-RAY DIFFRACTIONf_plane_restr0.0081336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6483-2.71450.36331030.32291314X-RAY DIFFRACTION68
2.7145-2.78790.31371310.29581667X-RAY DIFFRACTION87
2.7879-2.86990.34851370.28641744X-RAY DIFFRACTION91
2.8699-2.96250.29581440.28381830X-RAY DIFFRACTION93
2.9625-3.06840.32551450.29141863X-RAY DIFFRACTION96
3.0684-3.19120.28351490.25491902X-RAY DIFFRACTION98
3.1912-3.33640.31271500.24751913X-RAY DIFFRACTION98
3.3364-3.51220.25211490.23241886X-RAY DIFFRACTION98
3.5122-3.73210.21771470.21831876X-RAY DIFFRACTION97
3.7321-4.02010.22471500.19151907X-RAY DIFFRACTION98
4.0201-4.42430.18421480.19881885X-RAY DIFFRACTION97
4.4243-5.06370.18361490.19971896X-RAY DIFFRACTION97
5.0637-6.37640.28841450.21871838X-RAY DIFFRACTION95
6.3764-43.33950.21461490.19491912X-RAY DIFFRACTION98

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