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- PDB-4j1g: Leanyer orthobunyavirus nucleoprotein-ssRNA complex -

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Basic information

Entry
Database: PDB / ID: 4j1g
TitleLeanyer orthobunyavirus nucleoprotein-ssRNA complex
Components
  • Nucleocapsid
  • RNA (45-MER)
KeywordsVIRAL PROTEIN/RNA / PROTEIN-RNA COMPLEX / RNA binding protein / RNA binding / nucleocapsid protein / VIRAL PROTEIN-RNA 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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesLeanyer virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.789 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 1.2Feb 28, 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: Nucleocapsid
D: Nucleocapsid
C: Nucleocapsid
B: Nucleocapsid
E: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)118,9135
Polymers118,9135
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20940 Å2
ΔGint-181 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.839, 73.832, 79.884
Angle α, β, γ (deg.)69.74, 89.66, 75.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleocapsid


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: RNA chain RNA (45-MER)


Mass: 13732.498 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1-0.2 mM ammonium citrate tribasic (pH 7.0) and 15 - 18% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→48.047 Å / Num. all: 25492 / Num. obs: 23912 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.78→2.88 Å / % possible all: 69

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
X2DFmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
X2DFphasing
RefinementMethod to determine structure: SAD / Resolution: 2.789→48.047 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1998 8.36 %
Rwork0.2333 --
obs0.2367 23912 93.18 %
all-25492 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.789→48.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 881 0 62 8155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148348
X-RAY DIFFRACTIONf_angle_d1.44511469
X-RAY DIFFRACTIONf_dihedral_angle_d17.1793224
X-RAY DIFFRACTIONf_chiral_restr0.0771304
X-RAY DIFFRACTIONf_plane_restr0.0081326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.789-2.85840.3514930.33111027X-RAY DIFFRACTION62
2.8584-2.93570.38421200.31921314X-RAY DIFFRACTION77
2.9357-3.0220.35231290.33631403X-RAY DIFFRACTION86
3.022-3.11960.36621460.31381601X-RAY DIFFRACTION92
3.1196-3.2310.32071460.30741587X-RAY DIFFRACTION96
3.231-3.36040.36291520.29591676X-RAY DIFFRACTION98
3.3604-3.51330.37061500.28481653X-RAY DIFFRACTION99
3.5133-3.69840.29491490.26981633X-RAY DIFFRACTION99
3.6984-3.93010.32111530.25771676X-RAY DIFFRACTION99
3.9301-4.23330.27781510.21621653X-RAY DIFFRACTION99
4.2333-4.6590.2531510.21471667X-RAY DIFFRACTION99
4.659-5.33240.27691530.2131672X-RAY DIFFRACTION100
5.3324-6.71540.24791530.21941682X-RAY DIFFRACTION100
6.7154-48.05420.19371520.181670X-RAY DIFFRACTION99

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