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- PDB-8axf: Crystal structure of FMV N bound to 42-mer ssRNA -

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Basic information

Entry
Database: PDB / ID: 8axf
TitleCrystal structure of FMV N bound to 42-mer ssRNA
Components
  • Nucleocapsid protein
  • RNA (42-MER)
KeywordsVIRAL PROTEIN / nucleoprotein / genome packaging / virus / RNA / Fig Mosaic Virus
Function / homologyFimovirus nucleocapsid protein / viral nucleocapsid / RNA / RNA (> 10) / Nucleocapsid protein
Function and homology information
Biological speciesEmaravirus fici
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsIzhaki-Tavor, L. / Yechezkel, I. / Dessau, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation401/18 Israel
CitationJournal: Microbiol Spectr / Year: 2023
Title: RNA Encapsulation Mode and Evolutionary Insights from the Crystal Structure of Emaravirus Nucleoprotein.
Authors: Izhaki-Tavor, L.S. / Yechezkel, I.G. / Alter, J. / Dessau, M.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
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_PubMed / _citation.title
Revision 1.2Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein
Q: RNA (42-MER)
D: Nucleocapsid protein
C: Nucleocapsid protein
B: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,6529
Polymers153,4875
Non-polymers1654
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26370 Å2
ΔGint-284 kcal/mol
Surface area48980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.170, 151.820, 169.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleocapsid protein


Mass: 35168.285 Da / Num. of mol.: 4 / Fragment: nucleoprotein / Mutation: N45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emaravirus fici / Gene: NP / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: I2FFM8
#2: RNA chain RNA (42-MER)


Mass: 12814.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 20% PEG 3350 0.2 M Mg-formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.54→48.49 Å / Num. obs: 45871 / % possible obs: 99.1 % / Redundancy: 7.321 % / Biso Wilson estimate: 69.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.13 / Χ2: 0.865 / Net I/σ(I): 13.34 / Num. measured all: 335806 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.54-2.66.6651.5911.1717676302826520.5221.71887.6
2.6-2.77.4631.2491.7333981455345530.6491.344100
2.7-2.87.6810.9562.4830293394439440.7431.026100
2.8-2.97.5650.7163.4825600338433840.8280.771100
2.9-37.460.5854.5222207297929770.8820.63199.9
3-3.37.230.4187.2950148694069360.9170.45299.9
3.3-3.57.6440.29112.3825974340233980.960.31599.9
3.5-47.4020.15818.9143124582758260.9810.171100
4-4.57.2530.08326.3825719354735460.9940.09100
4.5-57.5420.06829.2417174227722770.9970.074100
5-5.57.270.06628.911174153815370.9960.07299.9
5.5-66.650.06627.687288109910960.9960.07199.7
6-77.0890.05730.69464133613350.9970.06299.9
7-87.2520.04634.8356207767750.9980.0599.9
8-106.7930.04337.4752447737720.9980.04799.9
10-206.090.04136.8945317477440.9980.04599.6
20-48.494.950.04633.445891291190.9970.05392.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AX4

8ax4


Resolution: 2.54→48.49 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 2000 4.36 %
Rwork0.2219 43826 -
obs0.2227 45826 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.49 Å2 / Biso mean: 82.2027 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.54→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 837 9 285 9387
Biso mean--100.87 83.97 -
Num. residues----1081
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.610.43281250.40292733285890
2.61-2.680.36091440.335831433287100
2.68-2.750.31681400.297430953235100
2.75-2.840.35441420.298931043246100
2.84-2.940.35291430.30431353278100
2.94-3.060.35081410.315530973238100
3.06-3.20.36291430.321931163259100
3.2-3.370.33241430.267931393282100
3.37-3.580.26681430.239631563299100
3.58-3.860.24271450.219631553300100
3.86-4.250.2021440.179431543298100
4.25-4.860.18811460.17532083354100
4.86-6.120.23771470.200432143361100
6.12-48.490.17551540.184433773531100
Refinement TLS params.Method: refined / Origin x: -27.7967 Å / Origin y: 5.9495 Å / Origin z: 60.7915 Å
111213212223313233
T0.382 Å2-0.0298 Å2-0.0186 Å2-0.4606 Å2-0.0211 Å2--0.4838 Å2
L0.1599 °20.0351 °2-0.0397 °2-0.2494 °20.4175 °2--0.9245 °2
S-0.0018 Å °-0.0206 Å °-0.0443 Å °-0.0421 Å °-0.0021 Å °0.0524 Å °-0.0638 Å °0.106 Å °0.0262 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA51 - 312
2X-RAY DIFFRACTION1allQ1 - 42
3X-RAY DIFFRACTION1allD52 - 314
4X-RAY DIFFRACTION1allC51 - 312
5X-RAY DIFFRACTION1allB53 - 401
6X-RAY DIFFRACTION1allE1 - 3
7X-RAY DIFFRACTION1allG2 - 323

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