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

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Basic information

Entry
Database: PDB / ID: 7nli
TitleS. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG2 variant
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 / MAD / Resolution: 3.119 Å
AuthorsCottee, M.A. / Letham, S.C. / 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)37,2943
Polymers37,2943
Non-polymers00
Water00
1
A: Ty1 Gag p22
B: Ty1 Gag p22


Theoretical massNumber of molelcules
Total (without water)24,8632
Polymers24,8632
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)24,8632
Polymers24,8632
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)280.890, 280.890, 40.405
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 351))
21(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))
31(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))

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 351))AA261 - 3023 - 44
12ILEILELYSLYS(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))AA304 - 32246 - 64
13LEULEUGLNGLN(chain A and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))AA324 - 35166 - 93
21SERSERILEILE(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))BB261 - 3023 - 44
22ILEILELYSLYS(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))BB304 - 32246 - 64
23LEULEUGLNGLN(chain B and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))BB324 - 35166 - 93
31SERSERILEILE(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))CC261 - 3023 - 44
32ILEILELYSLYS(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))CC304 - 32246 - 64
33LEULEUGLNGLN(chain C and (resid 261 through 302 or resid 304 through 322 or resid 324 through 351))CC324 - 35166 - 93

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Components

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


Mass: 12431.392 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 (E. coli) / Strain (production host): B834 / Variant (production host): DE3 / References: UniProt: P08405
Has ligand of interestN

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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: 6.42 Å3/Da / Density % sol: 80.86 % / Description: 80x80x250 um hexagonal prismic rod.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 260 nL Protein (13.6 mg/ml in 50 mM Sodium Acetate pH 5.0, 300 mM NaCl 1mM TCEP) 120 nL Mother Liquor (27.9% Glycerol, 17.7% PEG 4K 0.1M HEPES pH 7.5) 20 nL Seed solution (seeds in 20% ...Details: 260 nL Protein (13.6 mg/ml in 50 mM Sodium Acetate pH 5.0, 300 mM NaCl 1mM TCEP) 120 nL Mother Liquor (27.9% Glycerol, 17.7% PEG 4K 0.1M HEPES pH 7.5) 20 nL Seed solution (seeds in 20% Glycerol, 31% PEG 4K 0.1M HEPES pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97928, 0.97943, 0.97281
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979281
20.979431
30.972811
Reflection

Entry-ID: 7NLI / Diffraction-ID: 1 / % possible obs: 100 %

Resolution (Å)Num. obsRedundancy (%)CC1/2Rrim(I) allNet I/σ(I)Rpim(I) all
3.119-140.4531760112.80.9830.24624.5
3.5-92.172275655.40.9990.231160.042
3.41-81.172444255.50.9990.2316.50.042
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
3.119-3.33115.86.850590.760.1671.313
3.5-3.8356.75.2292710.1770.97
3.41-3.6856.55273610.1921.004

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
REFMAC5.8.0258refinement
Coot0.8.9.2model building
PDB_EXTRACT3.27data extraction
DIALS1.6.3data reduction
Aimless0.6.2data scaling
SHELXDE2018/1phasing
RefinementMethod to determine structure: MAD
Starting model: Ty1 p22

Resolution: 3.119→91.943 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 2.46 / Phase error: 27.54 / Stereochemistry target values: ML
Details: Refinement carried out using Peak wavelength (0.97928 A) dataset, with Friedel pairs separated to account for anomalous signal. Columns used: F_PEAK(+), SIGF_PEAK(+), F_PEAK(-), SIGF_PEAK(-) ...Details: Refinement carried out using Peak wavelength (0.97928 A) dataset, with Friedel pairs separated to account for anomalous signal. Columns used: F_PEAK(+), SIGF_PEAK(+), F_PEAK(-), SIGF_PEAK(-) or I_PEAK(+), SIGI_PEAK(+), I_PEAK(-), SIGI_PEAK(-). Experimentally measured F'=-8.15 and F''=6.44.
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1663 5.24 %Matches related structures
Rwork0.2334 30091 --
obs0.2346 31754 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.62 Å2 / Biso mean: 94.9444 Å2 / Biso min: 41.45 Å2
Refinement stepCycle: final / Resolution: 3.119→91.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 0 2203
Num. residues----274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A753X-RAY DIFFRACTION7.603TORSIONAL
12B753X-RAY DIFFRACTION7.603TORSIONAL
13C753X-RAY DIFFRACTION7.603TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.119-3.21070.38831520.33962430
3.2107-3.31440.31851300.33332539
3.3144-3.43280.32451310.29562522
3.4328-3.57030.3561310.29522502
3.5703-3.73280.32421190.27332556
3.7328-3.92960.27251150.2732498
3.9296-4.17580.29151400.21812522
4.1758-4.49820.22991680.21062519
4.4982-4.95090.2231310.20052484
4.9509-5.66720.22081430.21712529
5.6672-7.13960.28071730.22922453
7.1396-91.9430.18021300.18162537
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)
10.0334-0.01970.01040.0515-0.00970.0174-0.0134-0.08270.03280.00940.05310.09730.0024-0.0324-0.06741.07210.74130.2269-0.06240.44780.3594124.592230.4999-18.1608
20.08490.0410.00340.0180.00240.01290.1116-0.0028-0.23-0.07690.09260.1837-0.1369-0.10470.00921.05250.25560.015-0.15220.33970.4924125.096414.1681-38.6563
30.02350.02240.00520.0523-0.01580.01230.02560.014-0.1157-0.02970.02220.0268-0.1281-0.033-0.01781.02390.8844-0.09390.15120.27420.4736115.901157.8377-13.6544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 261 through 351)A261 - 351
2X-RAY DIFFRACTION2(chain 'B' and resid 261 through 352)B261 - 352
3X-RAY DIFFRACTION3(chain 'C' and resid 261 through 351)C261 - 351

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