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- PDB-4j4r: Hexameric SFTSVN -

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Basic information

Entry
Database: PDB / ID: 4j4r
TitleHexameric SFTSVN
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / nucleocapsid protein / nucleoprotein / nucleocapsid
Function / homology
Function and homology information


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
Biological speciesPhlebovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. ...Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of severe Fever with thrombocytopenia syndrome virus nucleocapsid protein in complex with suramin reveals therapeutic potential
Authors: Jiao, L. / Ouyang, S. / Liang, M. / Niu, F. / Shaw, N. / Wu, W. / Ding, W. / Jin, C. / Peng, Y. / Zhu, Y. / Zhang, F. / Wang, T. / Li, C. / Zuo, X. / Luan, C.H. / Li, D. / Liu, Z.J.
History
DepositionFeb 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)27,2891
Polymers27,2891
Non-polymers00
Water5,567309
1
A: Nucleocapsid protein
x 6


Theoretical massNumber of molelcules
Total (without water)163,7376
Polymers163,7376
Non-polymers00
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 area19950 Å2
ΔGint-113 kcal/mol
Surface area66820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.995, 103.995, 48.866
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

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Components

#1: Protein Nucleocapsid protein / SFTSVN


Mass: 27289.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebovirus / Strain: JS2010-018 / Production host: Escherichia coli (E. coli) / References: UniProt: I6WJ72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8% PEG 8000, 0.1 M NaAc, 0.2 M ZnAc2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 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: 1.9→45.031 Å / Num. all: 22407 / Num. obs: 21239 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.95 Å / % possible all: 61.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIXphenix.refine: 1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OV9

3ov9


Resolution: 1.9→45.031 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8861 / SU ML: 0.15 / σ(F): 1.39 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1168 5.21 %RANDOM
Rwork0.1789 21239 --
obs0.1802 21239 93.35 %-
all-22407 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.88 Å2 / Biso mean: 24.5798 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 309 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071952
X-RAY DIFFRACTIONf_angle_d1.0192643
X-RAY DIFFRACTIONf_chiral_restr0.066300
X-RAY DIFFRACTIONf_plane_restr0.005336
X-RAY DIFFRACTIONf_dihedral_angle_d13.033724
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 (%)
1.8996-1.9860.2444910.19131890198167
1.986-2.09070.21911360.1932343247983
2.0907-2.22170.21881710.17762705287697
2.2217-2.39320.22191530.179628382991100
2.3932-2.6340.2251410.188428312972100
2.634-3.01510.19641550.18828473002100
3.0151-3.79850.19631580.163728653023100
3.7985-45.04380.1851630.177729203083100

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