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- PDB-4j4x: Crystal structure of GraVN -

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Basic information

Entry
Database: PDB / ID: 4j4x
TitleCrystal structure of GraVN
ComponentsNP protein
KeywordsVIRAL PROTEIN / nucleocapsid protein / nucleoprotein
Function / homology
Function and homology information


viral nucleocapsid / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding / cytoplasm
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesGranada virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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: NP protein
B: NP protein
C: NP protein
D: NP protein
E: NP protein
F: NP protein


Theoretical massNumber of molelcules
Total (without water)170,6226
Polymers170,6226
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19410 Å2
ΔGint-126 kcal/mol
Surface area64620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.289, 96.337, 100.800
Angle α, β, γ (deg.)64.57, 81.72, 85.10
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.881928, 0.360377, -0.303862), (0.029837, 0.600646, 0.798958), (0.470439, -0.71369, 0.518974)39.71118, -87.68577, 13.3937
3given(0.664115, 0.744626, -0.066963), (0.353214, -0.233555, 0.90592), (0.658932, -0.625288, -0.41812)33.44183, -125.49677, 98.46086
4given(0.52546, 0.776533, 0.34769), (0.770501, -0.607633, 0.192641), (0.36086, 0.16667, -0.917606)-1.68629, -82.41505, 174.93008
5given(0.790101, 0.304869, 0.531785), (0.611438, -0.330542, -0.718948), (-0.043407, 0.893195, -0.44757)-35.23269, 25.65343, 158.20963
6given(0.837456, -0.160501, 0.522404), (0.513764, 0.557102, -0.652444), (-0.186314, 0.814786, 0.549009)-48.4425, 28.25651, 64.0798

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Components

#1: Protein
NP protein / nucleocapsid protein


Mass: 28436.949 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Granada virus / Production host: Escherichia coli (E. coli) / References: UniProt: E2DQZ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MgCl2, 21% PEG 1000, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 2.51→49.64 Å / Num. all: 56301 / Num. obs: 54500 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.51→2.54 Å / % possible all: 87.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4R

4j4r


Resolution: 2.51→49.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 0.011 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26641 2905 5.1 %RANDOM
Rwork0.19535 ---
obs0.19888 54499 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20.01 Å2
2--0.1 Å2-0.2 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11558 0 0 179 11737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211768
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211650
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.97515893
X-RAY DIFFRACTIONr_angle_other_deg0.828326902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25251485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05124.51459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.912152195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0961566
X-RAY DIFFRACTIONr_chiral_restr0.0880.21827
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022475
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 160 -
Rwork0.273 3456 -
obs--81.51 %

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