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- PDB-4j4y: Triple mutant GraVN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4j4y
TitleTriple mutant 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: 2.45 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 1.0Jun 12, 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


Theoretical massNumber of molelcules
Total (without water)113,5794
Polymers113,5794
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-90 kcal/mol
Surface area44030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.160, 76.798, 77.156
Angle α, β, γ (deg.)82.79, 69.51, 69.36
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999997, 0.000726, 0.002332), (0.000725, -1, 0.000408), (0.002332, -0.000406, -0.999997)-0.09105, 8.6045, 78.20092

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Components

#1: Protein
NP protein / nucleocapsid protein


Mass: 28394.707 Da / Num. of mol.: 4 / Mutation: R69D, K72E, K79E
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.: 115 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Ca(OAc)2, 12%(w/v) PEG3350, 0.04M citric acid, 0.06M Bis-tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.536
11H,H-K,H-L20.464
ReflectionResolution: 2.45→28.83 Å / Num. all: 37743 / Num. obs: 35932 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 91.7

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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: 2.45→28.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / SU B: 12.916 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.701 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29102 2046 5.4 %RANDOM
Rwork0.20981 ---
obs0.21412 35931 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.34 Å2-0.15 Å2
2--0.27 Å20.07 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7727 0 0 115 7842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027874
X-RAY DIFFRACTIONr_bond_other_d0.0010.027701
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.97410646
X-RAY DIFFRACTIONr_angle_other_deg0.875317801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4075994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20824.984319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.139151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.721540
X-RAY DIFFRACTIONr_chiral_restr0.0870.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021638
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.454→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 96 -
Rwork0.288 1829 -
obs--65.12 %
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)
10.0276-0.049-0.08240.1540.22950.51810.0165-0.0056-0.0128-0.02430.0953-0.0299-0.02540.0591-0.11190.0255-0.0276-0.02310.1445-0.02150.1572-11.7795-13.075121.1739
20.26350.2204-0.06950.2923-0.03920.0253-0.0371-0.0296-0.0434-0.1920.0172-0.0038-0.0334-0.00750.01990.31390.054-0.02460.14080.03470.0199-6.2103-11.724155.9833
30.0055-0.0158-0.02470.11990.23450.56910.0099-0.01740.0086-0.00450.0911-0.032-0.00470.0749-0.10110.0203-0.0003-0.02230.1543-0.01390.1595-11.864621.774256.7698
40.2376-0.16220.06430.1711-0.02610.0263-0.00470.020.03170.1366-0.0106-0.00290.048-0.0170.01530.3228-0.08890.01420.12410.03860.0215-6.157320.363622.0911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 250
2X-RAY DIFFRACTION2B3 - 250
3X-RAY DIFFRACTION3C3 - 250
4X-RAY DIFFRACTION4D3 - 250

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