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- PDB-4ijs: Crystal structure of nucleocapsid protein encoded by the prototyp... -

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Basic information

Entry
Database: PDB / ID: 4ijs
TitleCrystal structure of nucleocapsid protein encoded by the prototypic member of orthobunyavirus
Components
  • Nucleoprotein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / nucleocapsid protein / RNA binding / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


helical viral capsid / symbiont-mediated suppression of host gene expression / 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
Biological speciesBunyamwera virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsLi, B.B. / Wang, Q. / Lou, Z.Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Bunyamwera virus possesses a distinct nucleocapsid protein to facilitate genome encapsidation
Authors: Li, B.B. / Wang, Q. / Pan, X. / Fernandez de Castro, I. / Sun, Y. / Guo, Y. / Tao, X. / Risco, C. / Sui, S.F. / Lou, Z.Y.
History
DepositionDec 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
F: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
G: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)126,5998
Polymers126,5998
Non-polymers00
Water43224
1
A: Nucleoprotein
E: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

A: Nucleoprotein
E: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

A: Nucleoprotein
E: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

A: Nucleoprotein
E: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)126,5998
Polymers126,5998
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area21840 Å2
ΔGint-78 kcal/mol
Surface area44860 Å2
MethodPISA
2
B: Nucleoprotein
F: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

B: Nucleoprotein
F: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

B: Nucleoprotein
F: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

B: Nucleoprotein
F: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)126,5998
Polymers126,5998
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
3
C: Nucleoprotein
G: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

C: Nucleoprotein
G: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

C: Nucleoprotein
G: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

C: Nucleoprotein
G: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)126,5998
Polymers126,5998
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area20830 Å2
ΔGint-84 kcal/mol
Surface area45730 Å2
MethodPISA
4
D: Nucleoprotein
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

D: Nucleoprotein
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

D: Nucleoprotein
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

D: Nucleoprotein
H: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)126,5998
Polymers126,5998
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area21610 Å2
ΔGint-60 kcal/mol
Surface area43990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.140, 106.140, 485.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 28402.594 Da / Num. of mol.: 4 / Mutation: N83S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bunyamwera virus / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: P16495
#2: RNA chain
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3247.100 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.85 Å3/Da / Density % sol: 56.91 %

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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: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 24235 / Num. obs: 23406 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 96.43 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→40.746 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.772 / SU ML: 0.47 / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 1109 5.19 %
Rwork0.22 --
obs0.2229 21373 90.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.98 Å2 / Biso mean: 68.4184 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 814 0 24 8298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118593
X-RAY DIFFRACTIONf_angle_d1.54811794
X-RAY DIFFRACTIONf_dihedral_angle_d19.983271
X-RAY DIFFRACTIONf_chiral_restr0.1011326
X-RAY DIFFRACTIONf_plane_restr0.0061333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2003-3.34580.33491330.27122552268593
3.3458-3.52220.3441560.25062531268793
3.5222-3.74270.27961430.22262549269293
3.7427-4.03140.31391350.21462571270693
4.0314-4.43670.27931410.18972557269892
4.4367-5.07760.25081530.1952552270591
5.0776-6.39330.2651440.23312547269190
6.3933-40.74920.25091040.22612405250979

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