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- PDB-7nlg: S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG2 varian... -

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Basic information

Entry
Database: PDB / ID: 7nlg
TitleS. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG2 variant A273V mutant
ComponentsTy1 Gag p22
KeywordsVIRUS LIKE PARTICLE / Restriction factor / Ty1 / Gag / CA
Function / homologyTy transposon capsid protein / Ty transposon capsid protein / RNA binding / cytoplasm / Transposon TyH3 Gag polyprotein
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.528 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)36,9563
Polymers36,9563
Non-polymers00
Water00
1
A: Ty1 Gag p22
B: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)24,6382
Polymers24,6382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area9660 Å2
MethodPISA
2
C: Ty1 Gag p22

C: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)24,6382
Polymers24,6382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.873, 279.873, 39.923
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
11(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))
21(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))
31(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILE(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))AA261 - 3023 - 44
12ILEILELYSLYS(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))AA304 - 32246 - 64
13LEULEUGLNGLN(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))AA324 - 35066 - 92
21SERSERILEILE(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))BB261 - 3023 - 44
22ILEILELYSLYS(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))BB304 - 32246 - 64
23LEULEUGLNGLN(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))BB324 - 35066 - 92
31SERSERILEILE(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))CC261 - 3023 - 44
32ILEILELYSLYS(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))CC304 - 32246 - 64
33LEULEUGLNGLN(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 350))CC324 - 35066 - 92

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Components

#1: Protein Ty1 Gag p22 / Gag CA-CTD / AUG2 variant / Capsid protein / Ty1 p22 restriction factor


Mass: 12318.759 Da / Num. of mol.: 3 / Mutation: A273V
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: 6.48 Å3/Da / Density % sol: 81.02 % / Description: Hexagonal prisms or rods
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.59
Details: 200 nL Protein (30 mg/ml in 20 mM Tris HCl pH 9.0, 150 mM NaCl 1mM TCEP) 200 nL Mother Liquor (1.16M Li2SO4, 0.1M MES pH 6.59)
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 3.528→91.61 Å / Num. obs: 11994 / % possible obs: 100 % / Redundancy: 54 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.146 / Net I/σ(I): 17.7
Reflection shellResolution: 3.53→3.59 Å / Redundancy: 30.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 596 / Rpim(I) all: 0.43 / Rrim(I) all: 2.379 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
REFMAC5.8.0258refinement
Coot0.8.9.2model building
PDB_EXTRACT3.27data extraction
DIALS1.14.13data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ty1 p22

Resolution: 3.528→91.61 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 630 5.27 %Matches related structures
Rwork0.2246 11323 --
obs0.2268 11953 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 374.64 Å2 / Biso mean: 187.6009 Å2 / Biso min: 82.76 Å2
Refinement stepCycle: final / Resolution: 3.528→91.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 0 0 2178
Num. residues----270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A780X-RAY DIFFRACTION7.449TORSIONAL
12B780X-RAY DIFFRACTION7.449TORSIONAL
13C780X-RAY DIFFRACTION7.449TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5283-3.80080.36311040.29220999
3.8008-4.18320.31731210.22712204100
4.1832-4.78850.2321270.19682219100
4.7885-6.03290.27751410.23772255100
6.0329-91.610.2641370.21952436100
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)
10.9579-0.1214-0.02220.54190.22850.1098-0.2283-0.53590.18610.54910.36780.37450.65280.23880.03461.7310.25540.10550.54140.25491.1244123.952330.1161-18.079
21.92241.22610.33911.32820.48630.2264-0.09660.5086-1.2889-1.27950.3750.1906-0.35650.06460.17012.14060.2718-0.16140.80440.24031.6974125.361414.2948-38.2018
30.19450.27070.12741.16860.11680.15210.30780.3939-0.2838-0.7635-0.04970.1279-0.8556-0.44810.72142.43031.9239-0.03190.7780.46831.6605114.40357.1636-13.4652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 261 through 350)A261 - 350
2X-RAY DIFFRACTION2(chain 'B' and resid 261 through 350)B261 - 350
3X-RAY DIFFRACTION3(chain 'C' and resid 261 through 350)C261 - 350

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