PDB-4u5z: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1

ID or keywords:

Entry

Database: PDB / ID: 4u5z

Title

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1

Components

Structural protein VP1

Keywords

VIRAL PROTEIN / viral coat protein / jelly-roll fold / glycan binding

Function / homology

Function and homology information

T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function

Biological species

Trichodysplasia spinulosa-associated polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Stroh, L.J. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2015
Title: Trichodysplasia spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids.
Authors: Stroh, L.J. / Gee, G.V. / Blaum, B.S. / Dugan, A.S. / Feltkamp, M.C. / Atwood, W.J. / Stehle, T.

History

Deposition	Jul 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4u5z.cif.gz	1006.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4u5z.ent.gz	840.7 KB	Display	PDB format
PDBx/mmJSON format	4u5z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u5/4u5z ftp://data.pdbj.org/pub/pdb/validation_reports/u5/4u5z	HTTPS FTP

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Related structure data

Related structure data	4u60C 4u61C 4u62C 4fmgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4u61-2 6hku-1 6y61-2 4u62-2 6y6a-3 4u61-1 6y6a-4 6hkv-2 3bwq-d 4fmi-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5)

Deposited unit

A: Structural protein VP1

B: Structural protein VP1

C: Structural protein VP1

D: Structural protein VP1

E: Structural protein VP1

F: Structural protein VP1

G: Structural protein VP1

H: Structural protein VP1

I: Structural protein VP1

J: Structural protein VP1

310 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Structural protein VP1

B: Structural protein VP1

C: Structural protein VP1

D: Structural protein VP1

E: Structural protein VP1

defined by author&software
155 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Structural protein VP1

G: Structural protein VP1

H: Structural protein VP1

I: Structural protein VP1

J: Structural protein VP1

defined by author&software
155 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.100, 153.640, 143.980
Angle α, β, γ (deg.)	90.00, 91.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	45 - 102
2	1	1	4	B	45 - 102
3	1	1	4	C	45 - 102
4	1	1	4	D	45 - 102
5	1	1	4	E	45 - 102
6	1	1	4	F	45 - 102
7	1	1	4	G	45 - 102
8	1	1	4	H	45 - 102
9	1	1	4	I	45 - 102
10	1	1	4	J	45 - 102
1	2	1	4	A	101 - 185
2	2	1	4	B	101 - 185
3	2	1	4	C	101 - 185
4	2	1	4	D	101 - 185
5	2	1	4	E	101 - 185
6	2	1	4	F	101 - 185
7	2	1	4	G	101 - 185
8	2	1	4	H	101 - 185
9	2	1	4	I	101 - 185
10	2	1	4	J	101 - 185
1	3	1	4	A	190 - 302
2	3	1	4	B	190 - 302
3	3	1	4	C	190 - 302
4	3	1	4	D	190 - 302
5	3	1	4	E	190 - 302
6	3	1	4	F	190 - 302
7	3	1	4	G	190 - 302
8	3	1	4	H	190 - 302
9	3	1	4	I	190 - 302
10	3	1	4	J	190 - 302

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.995005, -0.035204, -0.093408), (-0.077484, 0.317577, -0.945062), (0.062934, 0.947579, 0.313263)	5.64911, 50.1354, 66.55419
3	given	(0.986776, -0.142179, -0.077835), (-0.160599, -0.792615, -0.588191), (0.021935, 0.592913, -0.804968)	2.24164, 2.58783, 134.99008
4	given	(0.986905, -0.160053, 0.020037), (-0.141212, -0.79725, 0.5869), (-0.077961, -0.582044, -0.809412)	-4.74613, -77.43385, 110.58089
5	given	(0.994983, -0.068312, 0.073094), (-0.048424, 0.310487, 0.949344), (-0.087546, -0.94812, 0.305621)	-6.48612, -78.51328, 27.22976
6	given	(0.999793, -0.017532, -0.010281), (-0.018358, -0.996069, -0.086658), (-0.008721, 0.086829, -0.996185)	-3.0085, -92.75861, 77.82016
7	given	(0.996777, 0.015534, 0.078707), (-0.065909, -0.400786, 0.913798), (0.04574, -0.91604, -0.39847)	-0.6986, -53.15814, 2.86626
8	given	(0.989773, 0.120325, 0.076623), (-0.140891, 0.740469, 0.657157), (0.022335, -0.661232, 0.749849)	6.86283, 30.81806, 17.08521
9	given	(0.987094, 0.158968, -0.019372), (-0.146197, 0.845132, -0.514178), (-0.065366, 0.510374, 0.857465)	10.08447, 42.83065, 101.96374
10	given	(0.993381, 0.080777, -0.081669), (-0.061562, -0.225863, -0.972212), (-0.096979, 0.970804, -0.219395)	4.72196, -33.3481, 139.68617

#1: Protein	Structural protein VP1 Mass: 30994.908 Da / Num. of mol.: 10 / Fragment: UNP residues 31-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichodysplasia spinulosa-associated polyomavirus Gene: VP1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2ESL7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM Na-malonate pH 5.0, 10% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2.1→30 Å / Num. obs: 158871 / % possible obs: 98.3 % / Redundancy: 4.7 % / B_iso Wilson estimate: 44.1 Å² / Net I/σ(I): 12
Reflection shell	Resolution: 2.1→2.16 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.7 / % possible all: 92.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
PHASER		phasing
XDS		data reduction
Coot		model building
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4FMG

4fmg

Resolution: 2.1→29.57 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.921 / SU B: 8.523 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24916	7970	5 %	RANDOM
R_work	0.20458	-	-	-
obs	0.20682	150901	98.31 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.085 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	30.05 Å²	0 Å²	-10.12 Å²
2-	-	5.74 Å²	-0 Å²
3-	-	-	-35.79 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→29.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20369	0	0	551	20920

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	20815
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19171
X-RAY DIFFRACTION	r_angle_refined_deg	1.273	1.966	28346
X-RAY DIFFRACTION	r_angle_other_deg	0.733	3	44184
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.263	5	2635
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.344	24.901	910
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.056	15	3323
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.121	15	92
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	3204
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	23876
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4612
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.914	6.525	10594
X-RAY DIFFRACTION	r_mcbond_other	2.914	6.525	10593
X-RAY DIFFRACTION	r_mcangle_it	3.441	8.764	13208
X-RAY DIFFRACTION	r_mcangle_other	3.441	8.764	13209
X-RAY DIFFRACTION	r_scbond_it	3.635	7.147	10221
X-RAY DIFFRACTION	r_scbond_other	3.635	7.147	10222
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.452	9.431	15137
X-RAY DIFFRACTION	r_long_range_B_refined	5.958	17.002	22501
X-RAY DIFFRACTION	r_long_range_B_other	5.96	16.929	22395
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3500 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.27	0.5
B	medium positional	0.31	0.5
C	medium positional	0.31	0.5
D	medium positional	0.3	0.5
E	medium positional	0.25	0.5
F	medium positional	0.3	0.5
G	medium positional	0.37	0.5
H	medium positional	0.29	0.5
I	medium positional	0.32	0.5
J	medium positional	0.31	0.5
A	medium thermal	2.68	2
B	medium thermal	2.8	2
C	medium thermal	3.06	2
D	medium thermal	2.73	2
E	medium thermal	2.89	2
F	medium thermal	3.18	2
G	medium thermal	2.83	2
H	medium thermal	3.03	2
I	medium thermal	3.47	2
J	medium thermal	3.36	2

LS refinement shell

Resolution: 2.101→2.156 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	575	-
R_work	0.271	10475	-
obs	-	-	92.58 %

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	2.5159	-0.1077	0.3161	0.7293	-0.079	1.5261	0.0052	0.2775	0.3002	-0.1195	-0.0721	0.0843	-0.1965	-0.1647	0.0669	0.1611	0.0391	0.0176	0.064	0.0219	0.2944	10.0202	-0.2785	46.724
2	0.439	0.0706	0.1795	0.9703	0.2138	0.8831	0.0072	0.0604	0.1135	-0.0569	-0.0429	0.0093	-0.1326	-0.0293	0.0357	0.1094	0.0074	0.0219	0.0143	0.0252	0.2453	16.3403	-4.0123	54.1228
3	8.1018	-0.9031	0.9563	2.1107	0.1455	0.2373	0.0994	-0.1943	-0.3766	-0.0927	-0.0264	0.5333	0.0442	-0.1374	-0.073	0.2038	-0.0349	0.0038	0.2489	0.0081	0.3329	-13.6619	-33.3757	42.3945
4	0.9456	0.0161	0.0285	0.7723	-0.1881	0.831	0.0012	0.1506	-0.1103	-0.0432	-0.0112	0.0313	0.0597	-0.0177	0.01	0.099	0.0274	0.0276	0.034	-0.0212	0.2438	13.756	-30.9364	45.0259
5	1.8808	0.4963	0.3631	0.9376	-0.044	1.0183	0.0467	-0.326	-0.2444	0.1472	-0.0549	0.015	0.175	-0.0623	0.0081	0.2195	-0.0027	-0.0036	0.0578	0.0432	0.3231	11.7356	-51.0397	72.4605
6	0.8909	0.2295	-0.1872	0.5026	-0.0766	0.4713	0.0531	-0.0255	-0.1092	0.0533	-0.027	0.0318	0.0933	-0.0069	-0.0261	0.1467	0.0002	0.0126	0.0044	0.0259	0.306	10.5225	-45.4388	68.1959
7	4.947	0.9394	-0.0905	1.2467	-0.0857	0.941	0.0112	-0.4958	0.2196	0.2583	-0.0848	0.2309	-0.0254	-0.2844	0.0736	0.238	-0.0359	0.0444	0.2203	-0.0233	0.2576	7.6412	-22.0293	97.6331
8	0.5852	0.2489	0.0362	1.2811	-0.085	0.9888	0.0607	-0.1912	-0.052	0.2148	-0.084	0.0546	0.1157	-0.1138	0.0233	0.2013	-0.0526	0.0127	0.0905	0.0152	0.238	14.7766	-29.0789	90.3149
9	5.5887	-0.2295	-1.2859	0.8056	-0.0578	1.5095	0.0425	0.0985	0.2236	0.1324	-0.0614	0.1352	-0.1697	-0.2268	0.0189	0.1898	0.0129	0.0081	0.0441	-0.0347	0.2751	8.0023	6.2889	77.8897
10	0.6134	-0.1281	0.0339	0.7701	-0.1374	1.2006	0.004	-0.1019	0.0647	0.106	0.0029	0.0245	-0.1145	-0.0368	-0.0069	0.13	-0.0114	0.0047	0.0197	-0.0189	0.2551	16.7145	-2.8455	80.9012
11	5.8447	0.6523	0.9383	0.762	0.3724	0.8171	0.0222	-0.4171	-0.2372	0.1362	-0.0105	0.1779	0.3098	-0.2829	-0.0117	0.3261	-0.0163	0.0405	0.2253	0.0655	0.3639	6.145	-93.012	25.5131
12	1.0617	-0.0603	0.0186	1.0276	0.2282	1.0944	-0.0086	-0.0294	-0.2498	0.1377	0.0102	0.0503	0.3	0.0518	-0.0015	0.2695	0.0519	0.0099	0.1045	-0.0049	0.3203	17.9942	-91.4184	16.6885
13	0.3275	0.1802	0.1021	1.0585	-0.1101	1.3797	0.0034	-0.105	0.2115	0.0939	0.0095	0.0686	-0.1571	-0.0069	-0.0129	0.2139	-0.0078	-0.013	0.0767	-0.026	0.2938	15.2709	-59.3113	26.0063
14	1.3669	-0.2335	0.0946	1.1642	-0.1134	1.111	-0.032	-0.1304	-0.0218	0.0958	0.0375	0.0773	0.0143	-0.0024	-0.0055	0.184	0.0044	-0.0064	0.0866	-0.02	0.2568	14.0094	-68.3102	28.0617
15	2.5863	-0.0533	-0.1409	1.018	0.2157	0.9433	0.0246	0.249	0.2401	-0.1756	-0.045	0.0843	-0.2751	-0.0507	0.0203	0.4021	-0.0494	-0.0139	0.1121	0.0408	0.3484	12.6761	-42.2514	2.2104
16	0.9481	-0.1291	0.2767	0.9243	0.2071	0.6374	-0.0106	0.1218	0.1208	-0.132	0.0203	0.005	-0.2002	0.0302	-0.0097	0.2928	-0.0516	-0.0121	0.1009	0.0347	0.3047	13.5275	-49.0822	5.2939
17	0.4438	-0.2826	-0.2781	1.4459	0.1545	0.9907	0.0324	0.3125	0.0313	-0.2923	-0.0634	0.0277	-0.3761	0.031	0.031	0.4081	-0.04	-0.0059	0.3306	0.0046	0.291	17.1176	-62.4942	-19.3059
18	2.7753	-0.0852	0.2833	1.4023	0.1058	1.3332	-0.0007	0.2209	0.0962	-0.2408	-0.0172	0.2335	-0.3025	-0.0614	0.0179	0.3488	0.0442	-0.0271	0.2469	-0.0658	0.3012	8.7122	-68.561	-18.0644
19	0.4781	-0.2535	0.3179	0.9524	-0.0291	1.7377	0.0363	0.0455	-0.2258	-0.0665	0.0019	0.1706	0.2485	-0.0928	-0.0383	0.2429	0.0576	-0.0083	0.2081	-0.1299	0.4087	16.6216	-96.7523	-11.826
20	0.555	-0.0946	-0.0493	0.9791	0.0865	1.9654	0.0441	0.2131	-0.1179	-0.0766	-0.0488	0.1075	0.1145	-0.0137	0.0046	0.1715	0.0549	0.0011	0.1868	-0.109	0.3368	17.1028	-89.0666	-10.1666

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 122
2	X-RAY DIFFRACTION	2	A	123 - 303
3	X-RAY DIFFRACTION	3	B	33 - 49
4	X-RAY DIFFRACTION	4	B	50 - 303
5	X-RAY DIFFRACTION	5	C	34 - 100
6	X-RAY DIFFRACTION	6	C	101 - 303
7	X-RAY DIFFRACTION	7	D	33 - 68
8	X-RAY DIFFRACTION	8	D	69 - 302
9	X-RAY DIFFRACTION	9	E	32 - 68
10	X-RAY DIFFRACTION	10	E	69 - 302
11	X-RAY DIFFRACTION	11	F	33 - 64
12	X-RAY DIFFRACTION	12	F	65 - 303
13	X-RAY DIFFRACTION	13	G	34 - 147
14	X-RAY DIFFRACTION	14	G	148 - 302
15	X-RAY DIFFRACTION	15	H	33 - 102
16	X-RAY DIFFRACTION	16	H	108 - 303
17	X-RAY DIFFRACTION	17	I	33 - 239
18	X-RAY DIFFRACTION	18	I	240 - 302
19	X-RAY DIFFRACTION	19	J	34 - 109
20	X-RAY DIFFRACTION	20	J	110 - 302

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