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- PDB-4j4v: Pentameric SFTSVN with suramin -

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Basic information

Entry
Database: PDB / ID: 4j4v
TitlePentameric SFTSVN with suramin
ComponentsNucleocapsid proteinVirus
KeywordsVIRAL PROTEIN / nucleocapsid protein / nucleoprotein / nucleocapsid
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Chem-SVR / Nucleoprotein
Similarity search - Component
Biological speciesPhlebovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 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 1.2Mar 25, 2020Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
E: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,93410
Polymers136,4475
Non-polymers6,4865
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19760 Å2
ΔGint-206 kcal/mol
Surface area53120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.145, 154.888, 93.291
Angle α, β, γ (deg.)90.00, 102.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleocapsid protein / Virus / 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: Chemical
ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.67 Å3/Da / Density % sol: 53.93 %

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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: 2.3→42.72 Å / Num. all: 63182 / Num. obs: 60718 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.79 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 79.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4R

4j4r


Resolution: 2.303→42.717 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.7962 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1998 3.29 %RANDOM
Rwork0.2233 ---
obs0.2245 60718 96.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.22 Å2 / Biso mean: 51.5131 Å2 / Biso min: 20.11 Å2
Refinement stepCycle: LAST / Resolution: 2.303→42.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9389 0 165 250 9804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079752
X-RAY DIFFRACTIONf_angle_d1.05213251
X-RAY DIFFRACTIONf_chiral_restr0.0651475
X-RAY DIFFRACTIONf_plane_restr0.0041661
X-RAY DIFFRACTIONf_dihedral_angle_d15.2233654
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 (%)
2.3034-2.3610.3311130.28143313342676
2.361-2.42480.32031290.28213795392488
2.4248-2.49620.30361410.26664148428996
2.4962-2.57670.33431460.26764300444698
2.5767-2.66880.33221430.25994224436798
2.6688-2.77560.29621470.25264285443298
2.7756-2.90190.28141460.24994299444599
2.9019-3.05490.26651470.24594284443199
3.0549-3.24620.26711460.23864328447499
3.2462-3.49680.25851470.21754291443899
3.4968-3.84840.23891480.20384366451499
3.8484-4.40480.17811480.18564338448699
4.4048-5.54770.25251480.19814345449399
5.5477-42.72440.28031490.2214404455399
Refinement TLS params.Method: refined / Origin x: 39.2503 Å / Origin y: 10.2682 Å / Origin z: 21.2621 Å
111213212223313233
T0.298 Å2-0.0035 Å20.021 Å2-0.3032 Å20 Å2--0.1484 Å2
L0.3017 °20.0439 °20.1601 °2-0.6041 °2-0.0264 °2---0.1151 °2
S0.0099 Å °0.0175 Å °0.0169 Å °0.0415 Å °-0.0463 Å °0.0049 Å °0.0097 Å °0.0524 Å °0.0325 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 245
2X-RAY DIFFRACTION1ALLB2 - 245
3X-RAY DIFFRACTION1ALLC1 - 245
4X-RAY DIFFRACTION1ALLE2 - 245
5X-RAY DIFFRACTION1ALLD0 - 245
6X-RAY DIFFRACTION1ALLA301
7X-RAY DIFFRACTION1ALLB301
8X-RAY DIFFRACTION1ALLC301
9X-RAY DIFFRACTION1ALLE301
10X-RAY DIFFRACTION1ALLD301
11X-RAY DIFFRACTION1ALLA401 - 465
12X-RAY DIFFRACTION1ALLB401 - 438
13X-RAY DIFFRACTION1ALLC401 - 431
14X-RAY DIFFRACTION1ALLE401 - 447
15X-RAY DIFFRACTION1ALLD401 - 469

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