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- PDB-8p10: The crystal structure of the C-terminal domain of Mengla nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 8p10
TitleThe crystal structure of the C-terminal domain of Mengla nucleoprotein
Components
  • ALA-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • Nucleoprotein
KeywordsVIRAL PROTEIN / Nucleoprotein / Filovirus / Mengla
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / viral nucleocapsid / Nucleoprotein
Function and homology information
Biological speciesMengla dianlovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsFerrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117976GB-I00 Spain
CitationJournal: Microbiol Spectr / Year: 2023
Title: Structural insights on the nucleoprotein C-terminal domain of Mengla virus.
Authors: Ferrero, D.S. / Tomas Gilabert, O. / Verdaguer, N.
History
DepositionMay 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
V: Nucleoprotein
H: Nucleoprotein
Z: Nucleoprotein
B: Nucleoprotein
Y: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
T: Nucleoprotein
P: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
S: Nucleoprotein
I: Nucleoprotein
A: Nucleoprotein
X: Nucleoprotein
W: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
U: Nucleoprotein
a: Nucleoprotein
b: Nucleoprotein
O: Nucleoprotein
D: Nucleoprotein
c: ALA-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Theoretical massNumber of molelcules
Total (without water)400,48629
Polymers400,48629
Non-polymers00
Water0
1
E: Nucleoprotein
L: Nucleoprotein
K: Nucleoprotein
H: Nucleoprotein
B: Nucleoprotein
G: Nucleoprotein
C: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
I: Nucleoprotein
A: Nucleoprotein
J: Nucleoprotein
F: Nucleoprotein
D: Nucleoprotein
c: ALA-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Theoretical massNumber of molelcules
Total (without water)200,60015
Polymers200,60015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
V: Nucleoprotein
Z: Nucleoprotein
Y: Nucleoprotein
T: Nucleoprotein
P: Nucleoprotein
S: Nucleoprotein
X: Nucleoprotein
W: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein
U: Nucleoprotein
a: Nucleoprotein
b: Nucleoprotein
O: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)199,88614
Polymers199,88614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.309, 85.710, 146.241
Angle α, β, γ (deg.)88.519, 76.451, 80.258
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein ...
Nucleoprotein / / Nucleocapsid protein


Mass: 14277.541 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q1NMU1
#2: Protein/peptide ALA-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 714.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mengla dianlovirus / Production host: Escherichia coli (E. coli)

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M MES pH 6.5, 30% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.25→142.156 Å / Num. obs: 30881 / % possible obs: 89.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 104.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.2
Reflection shellResolution: 3.256→4.052 Å / Rmerge(I) obs: 0.713 / Num. unique obs: 6177 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
REFMACV.5refinement
PHENIXdev_4788refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→47.99 Å / SU ML: 0.4981 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.9231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3046 1573 5.1 %
Rwork0.2742 29255 -
obs0.2758 30828 62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.92 Å2
Refinement stepCycle: LAST / Resolution: 3.26→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15285 0 0 0 15285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004315704
X-RAY DIFFRACTIONf_angle_d0.722421384
X-RAY DIFFRACTIONf_chiral_restr0.04132280
X-RAY DIFFRACTIONf_plane_restr0.01112841
X-RAY DIFFRACTIONf_dihedral_angle_d12.84145992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.26-3.360.267340.350775X-RAY DIFFRACTION1.78
3.36-3.480.3961200.3787404X-RAY DIFFRACTION9.38
3.48-3.620.3445350.3869856X-RAY DIFFRACTION19.76
3.62-3.780.3459660.36011427X-RAY DIFFRACTION33.03
3.79-3.980.40681160.35182291X-RAY DIFFRACTION53.01
3.98-4.230.42051970.32293189X-RAY DIFFRACTION74.89
4.23-4.560.30322210.28214085X-RAY DIFFRACTION94.7
4.56-5.020.31072220.27784225X-RAY DIFFRACTION99.11
5.02-5.740.32422440.28864249X-RAY DIFFRACTION99.16
5.74-7.230.34452110.29524252X-RAY DIFFRACTION98.83
7.23-47.990.22742370.21484202X-RAY DIFFRACTION98.14

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