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- PDB-4xzc: The crystal structure of Kupe virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4xzc
TitleThe crystal structure of Kupe virus nucleoprotein
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / nucleoprotein / Kupe virus
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1110 / Nucleocapsid N protein / Nucleocapsid N protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesKupe virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsGuo, Y. / Wang, W. / Liu, X. / Wang, X. / Wang, J. / Huo, T. / Liu, B.
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Functional Diversity of Nairovirus-Encoded Nucleoproteins.
Authors: Wang, W. / Liu, X. / Wang, X. / Dong, H. / Ma, C. / Wang, J. / Liu, B. / Mao, Y. / Wang, Y. / Li, T. / Yang, C. / Guo, Y.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)108,3782
Polymers108,3782
Non-polymers00
Water1,65792
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)54,1891
Polymers54,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)54,1891
Polymers54,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.981, 73.981, 423.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 54188.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kupe virus / Production host: Escherichia coli (E. coli) / References: UniProt: B8PWH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200mM sodium nitrate (PH 8.0), 5mM cobalt chloride, 8% (wt/vol) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 37285 / % possible obs: 98.5 % / Redundancy: 11.3 % / Net I/σ(I): 20.92
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.296 / Num. measured obs: 19 / Rsym value: 0.42 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U3I

3u3i


Resolution: 2.601→49.059 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1999 5.38 %
Rwork0.2116 --
obs0.2153 37162 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→49.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 0 0 92 7432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097495
X-RAY DIFFRACTIONf_angle_d1.1510118
X-RAY DIFFRACTIONf_dihedral_angle_d15.662776
X-RAY DIFFRACTIONf_chiral_restr0.0421097
X-RAY DIFFRACTIONf_plane_restr0.0051299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6007-2.66580.36451330.27592336X-RAY DIFFRACTION94
2.6658-2.73790.3231360.25432382X-RAY DIFFRACTION96
2.7379-2.81840.29171360.2452400X-RAY DIFFRACTION97
2.8184-2.90940.32091380.25082434X-RAY DIFFRACTION97
2.9094-3.01330.33931390.25952447X-RAY DIFFRACTION98
3.0133-3.1340.3331410.26152471X-RAY DIFFRACTION99
3.134-3.27660.35711410.25932485X-RAY DIFFRACTION99
3.2766-3.44930.33841430.23872514X-RAY DIFFRACTION100
3.4493-3.66530.2961450.2312535X-RAY DIFFRACTION100
3.6653-3.94820.30381440.20492545X-RAY DIFFRACTION100
3.9482-4.34530.23971470.19492589X-RAY DIFFRACTION100
4.3453-4.97360.23651470.17532581X-RAY DIFFRACTION100
4.9736-6.26410.25531500.18952626X-RAY DIFFRACTION100
6.2641-49.06810.22731590.1732818X-RAY DIFFRACTION99

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