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- PDB-7xiv: Structural insight into the interactions between Lloviu virus VP3... -

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Basic information

Entry
Database: PDB / ID: 7xiv
TitleStructural insight into the interactions between Lloviu virus VP30 and nucleoprotein
ComponentsNucleocapsid protein,Minor nucleoprotein VP30
KeywordsVIRUS / Lloviu virus / VP30 / NP / Interaction
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / zinc ion binding
Similarity search - Function
Transcriptional activator VP30, Filoviridae type / Ebola virus-specific transcription factor VP30 / Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Transcriptional activator VP30
Similarity search - Component
Biological speciesLloviu cuevavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsDong, S.S. / Qin, X.C. / Sun, W.Y. / Luan, F.C. / Wang, J.J. / Ma, L. / Li, X.X. / Yang, G.X. / Hao, C.Y.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070267,31622007,31670237 China
Other governmentNational key R&DProgram of China (2018YFD1000501) China
Other governmentShandong Provincial Natural Science Foundation, China (ZR2019ZD48, ZR2020QC057) China
Other governmentTaishan Scholars Project (tsqn201812079) China
Other governmentHigher Educational Science and Technology Program of Jinan City (2020GXRC058) China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural insights into the interactions between lloviu virus VP30 and nucleoprotein.
Authors: Sun, W. / Luan, F. / Wang, J. / Ma, L. / Li, X. / Yang, G. / Hao, C. / Qin, X. / Dong, S.
History
DepositionApr 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein,Minor nucleoprotein VP30
B: Nucleocapsid protein,Minor nucleoprotein VP30


Theoretical massNumber of molelcules
Total (without water)38,7402
Polymers38,7402
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-42 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.251, 64.251, 175.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 30 through 154)
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 30 through 154)A30 - 154
211chain BB183 - 307

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Components

#1: Protein Nucleocapsid protein,Minor nucleoprotein VP30 / Nucleoprotein / Transcriptional activator VP30


Mass: 19369.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lloviu cuevavirus / Strain: isolate Bat/Spain/Asturias-Bat86/2003 / Production host: Expression vector pET-mod (others) / References: UniProt: G8EFI1, UniProt: G8EFI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 7.0, 0.25 M NaCl, 22% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.498→32.126 Å / Num. obs: 13571 / % possible obs: 100 % / Redundancy: 13.8 % / Rpim(I) all: 0.02 / Net I/σ(I): 40.4
Reflection shellResolution: 2.498→2.598 Å / Num. unique obs: 660 / Rpim(I) all: 0.084

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVW

5dvw


Resolution: 2.498→32.126 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 32.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 1299 10.01 %
Rwork0.229 11676 -
obs0.233 12975 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.15 Å2 / Biso mean: 63.953 Å2 / Biso min: 36 Å2
Refinement stepCycle: final / Resolution: 2.498→32.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 0 13 2034
Biso mean---54.83 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012056
X-RAY DIFFRACTIONf_angle_d1.2982786
X-RAY DIFFRACTIONf_chiral_restr0.07331
X-RAY DIFFRACTIONf_plane_restr0.008345
X-RAY DIFFRACTIONf_dihedral_angle_d9.5091244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1110X-RAY DIFFRACTION7.367TORSIONAL
12B1110X-RAY DIFFRACTION7.367TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4981-2.5980.34171340.2594118690
2.598-2.71620.32361290.29118791
2.7162-2.85930.37661380.2898123694
2.8593-3.03840.39191410.3034126996
3.0384-3.27270.36071440.2878128597
3.2727-3.60170.29631490.2642133399
3.6017-4.1220.24151500.2133134399
4.122-5.18970.23821520.18591372100

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