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- PDB-3ouo: Structure of the Nucleoprotein from Rift Valley Fever Virus -

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Basic information

Entry
Database: PDB / ID: 3ouo
TitleStructure of the Nucleoprotein from Rift Valley Fever Virus
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Orthogonal Bundle / Viral genomic RNA encapsidation / RNA Viral Nucleoprotein
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
NITRITE ION / Nucleoprotein
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFerron, F. / Danek, E.I. / Li, Z. / Luo, D. / Wong, Y.H. / Coutard, B. / Lantez, V. / Charrel, R. / Canard, B. / Walz, T. / Lescar, J.
CitationJournal: Plos Pathog. / Year: 2011
Title: The hexamer structure of Rift Valley fever virus nucleoprotein suggests a mechanism for its assembly into ribonucleoprotein complexes
Authors: Ferron, F. / Li, Z. / Danek, E.I. / Luo, D. / Wong, Y. / Coutard, B. / Lantez, V. / Charrel, R. / Canard, B. / Walz, T. / Lescar, J.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2296
Polymers84,0913
Non-polymers1383
Water6,251347
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules

A: Nucleoprotein
B: Nucleoprotein
hetero molecules

A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,45812
Polymers168,1826
Non-polymers2766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20120 Å2
ΔGint-115 kcal/mol
Surface area64220 Å2
MethodPISA
2
C: Nucleoprotein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)168,45812
Polymers168,1826
Non-polymers2766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area20080 Å2
ΔGint-130 kcal/mol
Surface area63130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.500, 175.500, 47.417
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 245
2114B2 - 245
3114C2 - 245

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 28030.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Strain: ZH-548 M12 / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: P21700
#2: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200mM MgNO3, 17% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→47.44 Å / Num. all: 37702 / Num. obs: 37672 / % possible obs: 99.98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 6
Reflection shellResolution: 2.3→2.42 Å / % possible all: 98.41

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.65 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.888 / SU B: 14.146 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24296 1881 5 %RANDOM
Rwork0.19708 ---
obs0.19941 35717 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 9 347 6078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9597991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5995744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26423.221267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.607151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8681553
X-RAY DIFFRACTIONr_chiral_restr0.0690.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4111.53679
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82325873
X-RAY DIFFRACTIONr_scbond_it1.30232233
X-RAY DIFFRACTIONr_scangle_it2.2784.52111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1829 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.980.5
2BMEDIUM POSITIONAL0.880.5
3CMEDIUM POSITIONAL0.860.5
1AMEDIUM THERMAL0.472
2BMEDIUM THERMAL0.412
3CMEDIUM THERMAL0.412
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 137 -
Rwork0.212 2616 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36070.12250.01860.17490.09230.1019-0.04190.0282-0.0078-0.04210.03060.0177-0.0413-0.00980.01130.0362-0.0029-0.00360.02160.00740.021516.63668.90644.408
21.0421-0.6085-0.10920.42930.10510.03530.0039-0.01990.02850.02150.0026-0.01320.0108-0.006-0.00650.02920.01880.00770.05030.01570.0257-18.5371.08944.39
31.0496-0.13110.0860.03730.0390.1343-0.0034-0.0364-0.01170.01640.01180.00220.04690.0074-0.00840.03510.01260.00950.02620.02680.03126.35633.96560.109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 24
2X-RAY DIFFRACTION1A25 - 109
3X-RAY DIFFRACTION1A110 - 245
4X-RAY DIFFRACTION2B3 - 24
5X-RAY DIFFRACTION2B25 - 109
6X-RAY DIFFRACTION2B110 - 245
7X-RAY DIFFRACTION3C3 - 24
8X-RAY DIFFRACTION3C25 - 109
9X-RAY DIFFRACTION3C110 - 245

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