PDB-9rxw: Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt

ID or keywords:

Entry

Database: PDB / ID: 9rxw

Title

Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt

Components

Capsid protein

Keywords

VIRUS LIKE PARTICLE / Capsid / Gag / Retrotransposon

Function / homology

Ty transposon capsid protein / Ty transposon capsid protein / viral translational frameshifting / RNA binding / cytoplasm / Transposon Ty1-MR1 Gag polyprotein

Function and homology information

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Cottee, M.A. / Taylor, I.A.

Funding support

United Kingdom, 3items

Citation

Journal: 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

Deposition	Jul 13, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9rxw.cif.gz	111.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9rxw.ent.gz	65.8 KB	Display	PDB format
PDBx/mmJSON format	9rxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9rxw_validation.pdf.gz	296.1 KB	Display	wwPDB validaton report
Full document	9rxw_full_validation.pdf.gz	297.1 KB	Display
Data in XML	9rxw_validation.xml.gz	7.3 KB	Display
Data in CIF	9rxw_validation.cif.gz	9.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rx/9rxw ftp://data.pdbj.org/pub/pdb/validation_reports/rx/9rxw	HTTPS FTP

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Related structure data

Related structure data	9rxxC 9rxyC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Capsid protein

B: Capsid protein

22.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Gel filtration shows single oligomeric species in solution, consistent with crystallographic dimer, and closely related orthologues

Unit cell

Length a, b, c (Å)	31.593, 34.332, 45.333
Angle α, β, γ (deg.)	101.641, 96.351, 109.279
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLN / End label comp-ID: GLN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 262 - 350 / Label seq-ID: 4 - 92

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Capsid protein / CA / Gag-p45 / p54 Mass: 11127.427 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RefSeq: NC_001134 Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TY1A-MR1, YMRCTy1-3 GAG, YMR046C, YM9532.11C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q04215
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2 Å³/Da / Density % sol: 38.65 % Description: Typically small angular shards, approx 70x30um. Grew overnight, harvested after 1 day
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 150 nL protein (12 mg/ml (1.067mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NaCl, 10% PEG3K, 0.1M Na Phos Citrate pH4.2)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 16, 2020
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.6→43.59 Å / Num. obs: 18863 / % possible obs: 82.6 % / Redundancy: 3.4 % / B_iso Wilson estimate: 20.42 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.034 / R_rim(I) all: 0.067 / Net I/σ(I): 20
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 3.1 % / Num. unique obs: 361 / CC_1/2: 0.492 / R_pim(I) all: 0.833 / R_rim(I) all: 1.524 / % possible all: 31.26

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Processing

Software

Name	Version	Classification
xia2	0.7.107-g95bc1153-dials-3.2	data reduction
DIALS	3.2.3-gcbf1028a5-release	data reduction
TRUNCATE	CCP4 7.1.008	data scaling
PHASER	2.8.3	phasing
ARP/wARP	8.0 patch 1	model building
Coot	0.9.8.1	model building
REFMAC	5.8.0340	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→43.577 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.96 / SU B: 5.719 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2022	978	5.193 %	Random selection
R_work	0.1798	17855	-	-
all	0.181	-	-	-
obs	-	18833	82.496 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.523 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.695 Å²	-0.722 Å²	-1.663 Å²
2-	-	0.886 Å²	-0.925 Å²
3-	-	-	0.062 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→43.577 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1417	0	0	74	1491

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	1508
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1338
X-RAY DIFFRACTION	r_angle_refined_deg	1.375	1.635	2057
X-RAY DIFFRACTION	r_angle_other_deg	0.489	1.561	3084
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.987	5	194
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.37	23.913	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.425	10.332	241
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.9	10	65
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	230
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1836
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	356
X-RAY DIFFRACTION	r_nbd_refined	0.239	0.2	388
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	1254
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	818
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.141	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.254	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.192	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.138	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.041	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.786	1.849	754
X-RAY DIFFRACTION	r_mcbond_other	1.785	1.848	754
X-RAY DIFFRACTION	r_mcangle_it	2.928	2.737	946
X-RAY DIFFRACTION	r_mcangle_other	2.929	2.74	947
X-RAY DIFFRACTION	r_scbond_it	2.759	2.12	754
X-RAY DIFFRACTION	r_scbond_other	2.757	2.122	755
X-RAY DIFFRACTION	r_scangle_it	4.082	3.079	1107
X-RAY DIFFRACTION	r_scangle_other	4.08	3.08	1108
X-RAY DIFFRACTION	r_lrange_it	6.442	29.693	1816
X-RAY DIFFRACTION	r_lrange_other	6.411	29.255	1814
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	2959

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09939	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09939	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.6-1.641	0.331	36	0.356	508	0.355	1701	0.909	0.899	31.9812	0.354
1.641-1.686	0.32	28	0.339	631	0.338	1653	0.932	0.922	39.8669	0.335
1.686-1.735	0.365	38	0.308	764	0.311	1598	0.912	0.924	50.1877	0.296
1.735-1.788	0.267	48	0.303	982	0.301	1534	0.939	0.939	67.1447	0.287
1.788-1.847	0.287	66	0.257	1261	0.259	1490	0.94	0.954	89.0604	0.23
1.847-1.912	0.26	80	0.203	1339	0.206	1490	0.963	0.972	95.2349	0.173
1.912-1.984	0.18	67	0.193	1275	0.192	1399	0.978	0.974	95.9257	0.167
1.984-2.064	0.261	66	0.18	1227	0.184	1340	0.963	0.979	96.4925	0.155
2.064-2.156	0.203	70	0.173	1213	0.175	1316	0.974	0.982	97.4924	0.148
2.156-2.261	0.24	56	0.156	1140	0.159	1230	0.956	0.986	97.2358	0.134
2.261-2.383	0.164	60	0.158	1093	0.158	1179	0.982	0.985	97.7947	0.138
2.383-2.527	0.189	48	0.152	1038	0.154	1111	0.981	0.986	97.7498	0.129
2.527-2.701	0.205	56	0.157	967	0.159	1046	0.973	0.985	97.8011	0.138
2.701-2.916	0.223	42	0.152	931	0.155	986	0.977	0.986	98.6815	0.136
2.916-3.193	0.212	39	0.162	838	0.165	896	0.977	0.984	97.8795	0.147
3.193-3.568	0.126	55	0.153	735	0.151	806	0.989	0.987	98.0149	0.144
3.568-4.115	0.172	41	0.168	662	0.168	709	0.985	0.983	99.1537	0.165
4.115-5.029	0.198	37	0.178	570	0.179	611	0.981	0.981	99.3453	0.184
5.029-7.065	0.283	26	0.263	430	0.264	463	0.968	0.972	98.4881	0.264
7.065-43.577	0.191	19	0.182	251	0.182	271	0.973	0.975	99.631	0.208

Refinement TLS params.

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

ID	L11 (°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)
1	1.5974	0.5737	1.0431	1.7273	-0.3399	2.0945	0.048	-0.0741	0.088	0.1493	-0.0522	0.0379	-0.0306	-0.0293	0.0042	0.0163	0.0002	0.0102	0.0103	0.0051	0.0219	0.361	-10.2419	7.3129
2	0.7123	0.253	0.1777	1.6577	1.0866	2.1445	-0.0495	0.0258	0.0371	-0.1466	0.0238	0.1315	-0.1148	0.0597	0.0257	0.0166	-0.0021	-0.0092	0.0186	0.0216	0.0408	-11.4591	-27.9007	-8.0865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	261 - 351
2	X-RAY DIFFRACTION	2	ALL	B	262 - 352

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