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- PDB-9rxy: Drt2, an Endogenised Ty1 Gag CA-CTD Restriction Factor, F323S Y329S -

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Basic information

Entry
Database: PDB / ID: 9rxy
TitleDrt2, an Endogenised Ty1 Gag CA-CTD Restriction Factor, F323S Y329S
ComponentsDomesticated Restriction of Ty1-Prime Relic 2 (Drt2)
KeywordsVIRUS LIKE PARTICLE / Restriction Factor / Capsid / Gag / Retrotransposon
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.184 Å
AuthorsCottee, M.A. / Taylor, I.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKCC2029 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2029 United Kingdom
Wellcome TrustCC2029 United Kingdom
CitationJournal: PLOS Genetics / Year: 2025
Title: Probing the molecular determinants of Ty1 transposition restriction specificity in yeast
Authors: Beckwith, S.L. / Cottee, M.A. / Hannon-Hatfield, J.A. / Newman, A.C. / Walker, E.C. / Romero, J.R. / Stoye, J.P. / Taylor, I.A. / Garfinkel, D.J.
History
DepositionJul 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)
B: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)
C: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)
D: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)


Theoretical massNumber of molelcules
Total (without water)46,6204
Polymers46,6204
Non-polymers00
Water00
1
A: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)
B: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)


Theoretical massNumber of molelcules
Total (without water)23,3102
Polymers23,3102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)
D: Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)


Theoretical massNumber of molelcules
Total (without water)23,3102
Polymers23,3102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.760, 38.833, 111.209
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Domesticated Restriction of Ty1-Prime Relic 2 (Drt2)


Mass: 11654.983 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: UWOPS05-227.2 / Gene: SCY_1152 / Production host: Escherichia coli BL21 (bacteria)
Has protein modificationN

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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: 41.73 %
Description: Small (~50-70 um) 3-dimensional crystals grew from phase-separation after 3-7 months.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 150 nL protein (45 mg/ml (3.88mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (20%PEG3350, 0.1M BisTris Propane, pH7.5, 0.2M NaF)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97948 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 20, 2022 / Details: Compound Refractive Lenses
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 3.184→110.461 Å / Num. obs: 4022 / % possible obs: 59.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 63.68 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.069 / Rrim(I) all: 0.176 / Net I/σ(I): 7.197
Reflection shellResolution: 3.184→3.535 Å / Redundancy: 6.63 % / Mean I/σ(I) obs: 1.203 / Num. unique obs: 202 / CC1/2: 0.534 / Rpim(I) all: 0.576 / Rrim(I) all: 1.49 / % possible all: 11.05

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Processing

Software
NameVersionClassification
XDSJan 10, 2022 (BUILT 20220110)data reduction
Aimless0.7.7data scaling
STARANISO2.3.79 (20211010)data scaling
PHASER2.8.3phasing
Coot0.9.8.1model building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.184→45.57 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3391 191 4.76 %Random selection
Rwork0.2999 ---
obs0.3017 4012 59.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.184→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 0 0 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022338
X-RAY DIFFRACTIONf_angle_d0.4463199
X-RAY DIFFRACTIONf_dihedral_angle_d2.985351
X-RAY DIFFRACTIONf_chiral_restr0.034394
X-RAY DIFFRACTIONf_plane_restr0.003428
LS refinement shellResolution: 3.184→45.57 Å
RfactorNum. reflection% reflection
Rfree0.3391 191 -
Rwork0.2999 3821 -
obs--59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6031-0.89850.05771.4592-0.05441.41740.29410.1593-0.0253-0.1598-0.19220.4272-0.1372-0.29380.7210.2250.06280.0870.291-0.15620.4724-14.286116.459747.0131
20.5762-0.02850.17010.9613-0.31940.74460.06980.2254-0.1358-0.1684-0.105-0.51490.01040.1251-0.48340.22590.19820.03150.2898-0.02750.35649.674619.056137.2911
30.46240.07760.54240.2719-0.31221.6745-0.1139-0.07210.1033-0.1249-0.0782-0.0324-0.390.2747-0.53920.90690.5447-0.02251.0296-0.02310.353324.479818.69712.6426
42.0102-0.2014-0.44290.0779-0.04760.44160.38320.6496-0.7383-0.4014-0.28150.20980.28690.1233-0.14560.87080.5439-0.20681.0268-0.13790.62639.4072-0.61912.4837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 261 through 350)
2X-RAY DIFFRACTION2(chain 'B' and resid 262 through 350)
3X-RAY DIFFRACTION3(chain 'C' and resid 262 through 347)
4X-RAY DIFFRACTION4(chain 'D' and resid 261 through 350)

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