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- PDB-4j4u: Pentamer SFTSVN -

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Basic information

Entry
Database: PDB / ID: 4j4u
TitlePentamer 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: 2.803 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
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
E: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)136,4475
Polymers136,4475
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16820 Å2
ΔGint-115 kcal/mol
Surface area54120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.188, 155.573, 97.656
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleocapsid protein / SFTSVN


Mass: 27289.492 Da / Num. of mol.: 5
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.: 59 / 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: 2.95 Å3/Da / Density % sol: 58.33 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→43.81 Å / Num. all: 35894 / Num. obs: 38804 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.86 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 92.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4R

4j4r


Resolution: 2.803→43.808 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7714 / SU ML: 0.43 / σ(F): 1.36 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1998 5.57 %RANDOM
Rwork0.1951 ---
obs0.1998 35894 92.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.1 Å2 / Biso mean: 36.5286 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: LAST / Resolution: 2.803→43.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 0 59 9539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019670
X-RAY DIFFRACTIONf_angle_d1.23613092
X-RAY DIFFRACTIONf_chiral_restr0.0811486
X-RAY DIFFRACTIONf_plane_restr0.0051661
X-RAY DIFFRACTIONf_dihedral_angle_d14.2323591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8034-2.87350.31071380.22072332247090
2.8735-2.95110.32351450.22162460260594
2.9511-3.0380.34871430.23012442258594
3.038-3.1360.32631450.22212455260095
3.136-3.2480.32351440.22372467261194
3.248-3.37810.34181460.2032465261194
3.3781-3.53170.2971450.19332469261494
3.5317-3.71780.25681430.18672413255693
3.7178-3.95060.29131430.18132421256493
3.9506-4.25540.24351430.16282435257892
4.2554-4.68320.22781420.15622406254892
4.6832-5.35990.23771420.17792406254891
5.3599-6.74890.30031400.20962375251590
6.7489-43.81310.25551390.21832350248988
Refinement TLS params.Method: refined / Origin x: -15.1412 Å / Origin y: -7.579 Å / Origin z: 22.1952 Å
111213212223313233
T0.112 Å20.0067 Å20.0103 Å2-0.1314 Å2-0.0116 Å2--0.0626 Å2
L0.2119 °2-0.0205 °20.0265 °2-0.2068 °2-0.0454 °2---0.0015 °2
S-0.0326 Å °-0.031 Å °0.0124 Å °0.0895 Å °-0.001 Å °-0.0122 Å °0.0174 Å °-0.0211 Å °-0.0093 Å °
Refinement TLS groupSelection details: all

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