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- PDB-7uln: Turnip yellows virus N-terminal readthrough domain -

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Basic information

Entry
Database: PDB / ID: 7uln
TitleTurnip yellows virus N-terminal readthrough domain
ComponentsMinor capsid protein P3-RTD
KeywordsVIRAL PROTEIN / Viral transmission / dimer / vector interaction
Function / homologyPotato leaf roll virus readthrough protein / Potato leaf roll virus readthrough protein / Luteovirus group 1 coat protein / Luteovirus coat protein / host cell plasmodesma / host cell periplasmic space / viral capsid / structural molecule activity / Readthrough protein P3-RTD
Function and homology information
Biological speciesTurnip yellows virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsSchiltz, C.J. / Chappie, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)2019-05200 United States
CitationJournal: Nat Commun / Year: 2022
Title: Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids
Authors: Schiltz, C.J. / Wilson, J.R. / Hosford, C.J. / Adams, M.C. / Preising, S.E. / DeBlasio, S.L. / MacLeod, H.J. / Van Eck, J. / Heck, M.L. / Chappie, J.S.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Minor capsid protein P3-RTD
B: Minor capsid protein P3-RTD


Theoretical massNumber of molelcules
Total (without water)53,8902
Polymers53,8902
Non-polymers00
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-23 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.434, 74.859, 130.779
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 Minor capsid protein P3-RTD / P74 / Readthrough protein / RT protein


Mass: 26945.105 Da / Num. of mol.: 2
Fragment: N-terminal readthrough domain (UNP residues 224-461)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip yellows virus / Gene: ORF3/ORF5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09514
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1 M HEPES, pH 7.7, 1.4 M ammonium sulfate, 0.1 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.53→130.78 Å / Num. obs: 69780 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 20.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.556.30.7292025732060.7320.310.7942.293.1
8.36-130.7860.04130625140.9990.0170.04562.399.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7ULO

7ulo


Resolution: 1.53→65.389 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 3428 4.92 %
Rwork0.174 66276 -
obs0.1751 69704 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.99 Å2 / Biso mean: 24.9293 Å2 / Biso min: 9.98 Å2
Refinement stepCycle: final / Resolution: 1.53→65.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 0 587 4327
Biso mean---33.58 -
Num. residues----472
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.53-1.54880.26021250.2207252492
1.5488-1.5720.23121510.20452708100
1.572-1.59650.23681300.2032768100
1.5965-1.62270.24931320.20152717100
1.6227-1.65070.25581270.19252764100
1.6507-1.68070.23331360.19522727100
1.6807-1.7130.24651510.20632759100
1.713-1.7480.25241380.20642724100
1.748-1.7860.26921380.20172798100
1.786-1.82760.25811240.19482717100
1.8276-1.87330.26231560.18692768100
1.8733-1.92390.21121530.18342741100
1.9239-1.98050.21231600.17942701100
1.9805-2.04450.17351490.16952757100
2.0445-2.11750.22111390.17322762100
2.1175-2.20230.17031480.17292778100
2.2023-2.30260.20641180.17172776100
2.3026-2.4240.21811380.17592798100
2.424-2.57580.21971660.18322769100
2.5758-2.77470.20111650.18152776100
2.7747-3.05390.17331360.18132795100
3.0539-3.49580.19071190.16332842100
3.4958-4.40420.14631420.1447285399
4.4042-65.3890.18121870.1681295499

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