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- PDB-8ax4: Crystal structure of FMV N in its RNA-free form -

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Basic information

Entry
Database: PDB / ID: 8ax4
TitleCrystal structure of FMV N in its RNA-free form
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / nucleoprotein / genome packaging / virus / RNA / Fig Mosaic Virus
Function / homologyFimovirus nucleocapsid protein / viral nucleocapsid / Nucleocapsid protein
Function and homology information
Biological speciesEmaravirus fici
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.28 Å
AuthorsIzhaki-Tavor, L. / Yechezkel, I. / Dessau, M.
Funding support Israel, 2items
OrganizationGrant numberCountry
Israel Science Foundation401/18 Israel
Other privateBARD IS-5270-20 R 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 30, 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein
D: Nucleocapsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7955
Polymers140,6734
Non-polymers1221
Water13,691760
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-105 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.870, 96.920, 103.520
Angle α, β, γ (deg.)90.000, 111.920, 90.000
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.45 mM Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.28→48.46 Å / Num. obs: 82002 / % possible obs: 98.8 % / Redundancy: 3.611 % / Biso Wilson estimate: 37.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.079 / Χ2: 0.84 / Net I/σ(I): 15.31 / Num. measured all: 296115 / Scaling rejects: 112
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
2.28-2.343.6431.6180.9421934607260210.5081.89799.2
2.34-2.43.7261.321.1522139599359410.5721.54299.1
2.4-2.473.7071.0251.4921270580357380.7021.298.9
2.47-2.553.6790.8021.8120458561155600.7890.93999.1
2.55-2.633.6830.6082.419932546054120.830.71299.1
2.63-2.733.6460.4493.2119056528852270.9120.52798.8
2.73-2.833.5450.344.0817883509250450.940.499.1
2.83-2.943.2380.2554.9315554493348040.9450.30697.4
2.94-3.073.7470.1927.2717486468446670.9810.22399.6
3.07-3.223.7840.12610.6717004452444940.9930.14799.3
3.22-3.43.7340.09513.6915781425942260.9940.1199.2
3.4-3.63.670.05720.5614765406140230.9980.06799.1
3.6-3.853.6030.0427.9613643384037870.9990.04798.6
3.85-4.163.3030.0333.9211411354934550.9990.03697.4
4.16-4.563.3650.02343.0810859330132270.9990.02797.8
4.56-5.13.6680.02246.9910767295829350.9990.02599.2
5.1-5.893.6270.02148.579471263526110.9990.02499.1
5.89-7.213.4470.01851.647562222521940.9990.02198.6
7.21-10.23.3450.01368.0256261756168210.01595.8
10.2-48.463.6870.01276.99351499295310.01496.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.28→48.46 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1927 2.51 %
Rwork0.2167 74799 -
obs0.2168 76726 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.34 Å2 / Biso mean: 42.789 Å2 / Biso min: 22.37 Å2
Refinement stepCycle: final / Resolution: 2.28→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8267 0 8 760 9035
Biso mean--46.22 46.4 -
Num. residues----1039
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 (%)
2.28-2.340.3158640.33372232229639
2.34-2.40.3738830.33253307339057
2.4-2.470.28641420.34445303544592
2.47-2.550.34061480.31657915939100
2.55-2.640.30061480.298657915939100
2.64-2.750.25241440.280657745918100
2.75-2.870.28331510.264458055956100
2.87-3.020.2581450.246258105955100
3.02-3.210.22291540.227557825936100
3.21-3.460.24651410.220658575998100
3.46-3.810.18151520.181957695921100
3.81-4.360.17911490.1625806595599
4.36-5.490.15851520.168758576009100
5.49-48.460.19771540.18735915606999
Refinement TLS params.Method: refined / Origin x: 31.0359 Å / Origin y: 26.0389 Å / Origin z: 14.1097 Å
111213212223313233
T0.2496 Å20.0172 Å20.0189 Å2-0.2747 Å20.0251 Å2--0.2858 Å2
L0.1423 °20.0926 °2-0.0105 °2-0.341 °20.153 °2--0.3133 °2
S0.0107 Å °0.0032 Å °-0.0209 Å °-0.0359 Å °-0.0429 Å °-0.0206 Å °-0.0177 Å °-0.0086 Å °0.0322 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 312
2X-RAY DIFFRACTION1allB52 - 310
3X-RAY DIFFRACTION1allC51 - 311
4X-RAY DIFFRACTION1allC337
5X-RAY DIFFRACTION1allD52 - 310
6X-RAY DIFFRACTION1allZ1 - 779

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