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- PDB-7nlh: S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG1 variant -

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Basic information

Entry
Database: PDB / ID: 7nlh
TitleS. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG1 variant
ComponentsTy1 Gag p22
KeywordsVIRUS LIKE PARTICLE / Restriction factor / Ty1 / Gag / CA
Function / homologyTy transposon capsid protein / Ty transposon capsid protein / viral translational frameshifting / RNA binding / cytoplasm / Transposon TyH3 Gag polyprotein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCottee, M.A. / Taylor, I.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)FC001178 United Kingdom
Wellcome TrustFC001178 United Kingdom
Cancer Research UKFC001178 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control.
Authors: Cottee, M.A. / Beckwith, S.L. / Letham, S.C. / Kim, S.J. / Young, G.R. / Stoye, J.P. / Garfinkel, D.J. / Taylor, I.A.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ty1 Gag p22
B: Ty1 Gag p22
C: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)40,3573
Polymers40,3573
Non-polymers00
Water00
1
A: Ty1 Gag p22
B: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)26,9042
Polymers26,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ty1 Gag p22

C: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)26,9042
Polymers26,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Unit cell
Length a, b, c (Å)282.124, 282.124, 39.967
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA261 - 34913 - 101
21GLUGLUBB261 - 34913 - 101
12GLNGLNAA261 - 35013 - 102
22GLNGLNCC261 - 35013 - 102
13GLUGLUBB261 - 34913 - 101
23GLUGLUCC261 - 34913 - 101

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ty1 Gag p22 / Gag CA-CTD / AUG1 variant / Capsid protein / Ty1 p22 restriction factor


Mass: 13452.185 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: TY1A, GAG, TYA1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08405

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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: 6.07 Å3/Da / Density % sol: 79.76 % / Description: 160x160x160 hexagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 300 nl protein (6.25 mg mL-1, in 20 mM Tris-HCl pH 8.5, 150 mM NaCl, 1 mM TCEP) 100 nl Mother Liquor (1.16 M Li2SO4, 0.1 M Tris-HCl pH 9.0) pH screened 7.5-9.0, Li2SO4 screened 1.125M-1.25M.
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97954 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.8→244.4 Å / Num. obs: 23876 / % possible obs: 100 % / Redundancy: 38.7 % / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 21.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 38.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3390 / CC1/2: 0.491 / Rpim(I) all: 0.627 / Rrim(I) all: 3.912 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.14_3260refinement
Coot0.8.9.2model building
PDB_EXTRACT3.27data extraction
DIALS1.14.5data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ty1 p22 Aug2 variant partial model

Resolution: 2.8→141.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.928 / SU B: 32.897 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 1259 5.3 %RANDOM
Rwork0.2564 ---
obs0.2568 22603 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 266.65 Å2 / Biso mean: 145.564 Å2 / Biso min: 94.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å21.92 Å20 Å2
2--3.85 Å20 Å2
3----12.48 Å2
Refinement stepCycle: final / Resolution: 2.8→141.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 0 0 2181
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172000
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.643012
X-RAY DIFFRACTIONr_angle_other_deg1.1811.5744633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34723.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9691515
X-RAY DIFFRACTIONr_chiral_restr0.050.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27770.07
12B27770.07
21A28010.09
22C28010.09
31B27730.09
32C27730.09
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 98 -
Rwork0.397 1651 -
all-1749 -
obs--99.89 %
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)
10.36970.2044-0.34510.1441-0.05331.04180.0299-0.0358-0.0944-0.14510.0118-0.0301-0.6899-0.1942-0.04171.79820.49060.15370.3640.11531.0968124.986830.5462-18.5226
22.61381.1143-2.43774.7318-0.08543.4003-0.05440.2459-0.3309-0.41180.03210.1803-0.3469-0.39420.02231.35240.1836-0.07660.27120.08661.2112126.202614.324-38.0438
32.2951-1.389-1.75779.38027.38866.04030.80740.3-0.1563-0.792-0.5689-0.5189-0.9074-0.5536-0.23852.82811.4250.04350.73050.07651.1109115.849457.8418-13.1412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A261 - 350
2X-RAY DIFFRACTION2B261 - 351
3X-RAY DIFFRACTION3C261 - 350

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