PDB-4jcd: S268Y Variant of JC Polyomavirus Major Capsid Protein VP1

ID or keywords:

Entry

Database: PDB / ID: 4jcd

Title

S268Y Variant of JC Polyomavirus Major Capsid Protein VP1

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / beta-sandwich / jelly roll topology / major capsid protein / PML-associated VP1 mutation

Function / homology

Function and homology information

T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function

Biological species

JC polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Stehle, T. / Stroh, L.J.

Citation

Journal: MBio / Year: 2013
Title: Progressive multifocal leukoencephalopathy-associated mutations in the JC polyomavirus capsid disrupt lactoseries tetrasaccharide c binding.
Authors: Maginnis, M.S. / Stroh, L.J. / Gee, G.V. / O'Hara, B.A. / Derdowski, A. / Stehle, T. / Atwood, W.J.

History

Deposition	Feb 21, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jcd.cif.gz	512 KB	Display	PDBx/mmCIF format
PDB format	pdb4jcd.ent.gz	424 KB	Display	PDB format
PDBx/mmJSON format	4jcd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jcd_validation.pdf.gz	476.2 KB	Display	wwPDB validaton report
Full document	4jcd_full_validation.pdf.gz	480.9 KB	Display
Data in XML	4jcd_validation.xml.gz	56.9 KB	Display
Data in CIF	4jcd_validation.cif.gz	82.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcd ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcd	HTTPS FTP

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Related structure data

Related structure data	4jceC 4jcfC 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4jcf-d 4we0-d 4jce-d 3nxd-d 4x16-d 4x0y-d 4x11-d 3nxg-d 6y5z-d 4x12-d 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: Major capsid protein VP1

B: Major capsid protein VP1

C: Major capsid protein VP1

D: Major capsid protein VP1

E: Major capsid protein VP1

hetero molecules

151 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	150.150, 96.180, 128.360
Angle α, β, γ (deg.)	90.00, 110.39, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.442756, 0.851745, 0.280175), (-0.855303, 0.30741, 0.41708), (0.269117, -0.424299, 0.864608)	11.4169, 20.32611, -5.64268
3	given	(-0.448973, 0.51511, 0.730127), (-0.529733, -0.811477, 0.246757), (0.719588, -0.275985, 0.637202)	31.8242, 14.58384, -15.81233
4	given	(-0.440764, -0.536269, 0.719821), (0.519811, -0.806263, -0.282376), (0.731795, 0.249709, 0.634131)	33.07157, -8.85358, -16.85943
5	given	(0.448737, -0.851329, 0.271799), (0.84759, 0.309044, -0.431374), (0.283243, 0.423947, 0.860257)	13.5618, -18.08582, -6.93917

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 Mass: 30151.955 Da / Num. of mol.: 5 / Mutation: S268Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) JC polyomavirus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03089
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1080 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 0.2 M KSCN, 12% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 15, 2012
Radiation	Monochromator: Bartels Monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→47 Å / Num. all: 114754 / Num. obs: 114754 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 25.7 Å² / Net I/σ(I): 12.6
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.57 / Num. unique all: 8396 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3NXG

3nxg

Resolution: 2→44.7 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.934 / SU B: 5.891 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20416	5758	5 %	RANDOM
R_work	0.16385	-	-	-
obs	0.16584	109011	99.36 %	-
all	-	114769	-	-

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: 19.278 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9965	0	42	1080	11087

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	10429
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.355	1.955	14224
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.28	5	1345
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.763	24.387	481
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.319	15	1677
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.963	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1595
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	8042
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.244	444	-
R_work	0.213	7932	-
obs	-	8376	98.63 %

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	0.946	-0.4112	1.4266	0.2785	-0.4443	2.6276	-0.0453	0.0211	0.002	-0.005	0.0417	-0.0282	-0.1836	0.0922	0.0036	0.0307	-0.0162	-0.014	0.0443	0.0106	0.0458	63.4499	15.3597	23.8844
2	0.1785	-0.1346	0.1852	0.2335	-0.1542	0.2925	-0.0345	0.046	0.0279	-0.0038	-0.0052	-0.0052	-0.0424	0.0498	0.0397	0.0159	-0.0178	-0.0084	0.0366	0.0178	0.0144	56.1432	10.6631	15.2808
3	0.1313	-0.1692	-0.0395	0.335	-0.1064	0.2257	0.0067	0.0228	-0.0218	-0.0149	-0.0442	0.0048	-0.0035	0.0179	0.0375	0.0084	-0.0154	-0.0059	0.0446	0.01	0.0356	54.2883	3.1842	11.7824
4	0.0613	-0.0088	0.0683	0.5592	0.1818	0.3083	-0.0206	0.0515	0.002	0.0334	-0.0284	-0.0173	0.0128	0.0343	0.0491	0.0101	-0.0186	0.0058	0.0519	0.0052	0.0305	58.6197	0.4356	17.7987
5	0.7656	-0.1273	0.8867	0.1228	-0.0364	1.2183	-0.0218	0.0223	-0.0091	-0.0022	0.0091	-0.0122	-0.043	0.0273	0.0128	0.0126	-0.0156	-0.0151	0.0264	0.0106	0.0338	59.5761	9.9919	24.5792
6	0.8807	0.0701	0.7357	0.029	-0.0367	1.2092	-0.0131	-0.0435	0.0794	0.0199	0.0218	0.0138	-0.1437	-0.0541	-0.0086	0.038	0.0067	0.0008	0.0343	-0.0122	0.0419	34.649	29.9842	35.7749
7	0.3282	-0.071	0.1226	0.0773	0.0818	0.5461	-0.0603	-0.0209	0.097	0.0004	-0.0056	0.0062	-0.0831	-0.0694	0.0659	0.0224	0.0058	-0.0258	0.0167	-0.0013	0.0471	39.2412	29.7973	29.6414
8	1.2419	0.4504	0.7158	0.3477	0.3356	0.4717	-0.011	0.0459	-0.0688	-0.0678	0.0782	-0.08	-0.0504	0.0018	-0.0672	0.0287	0.005	0.0248	0.0948	0.005	0.0281	18.8215	13.3449	19.5135
9	0.4368	-0.1147	0.0926	0.0441	0.0358	0.8417	-0.0197	-0.0105	0.0583	-0.0051	-0.0051	-0.0267	-0.0596	0.0104	0.0249	0.0301	-0.012	-0.0162	0.0155	0.0212	0.0425	46.4707	27.852	22.5506
10	0.3517	0.1428	0.3329	0.1371	0.1089	0.7302	-0.0261	0.0213	-0.0106	0.0155	0.0235	-0.0172	-0.0605	-0.0102	0.0026	0.0144	0.0086	-0.0094	0.0198	-0.0005	0.0337	36.8211	22.4905	34.3276
11	0.4792	0.2843	0.9131	0.5583	0.4418	1.7709	0.0051	-0.0782	-0.017	0.0983	0.0304	0.0465	-0.0254	-0.1817	-0.0355	0.0248	0.0196	0.0135	0.0662	-0.0051	0.0171	13.4377	4.1388	47.8579
12	0.0578	0.0747	0.0238	0.4088	0.0867	0.0741	0.0062	0.0094	0.0269	0.0284	-0.0133	0.0323	0.0264	-0.0494	0.0071	0.0179	-0.007	-0.0043	0.0629	-0.002	0.0177	13.537	7.0613	36.604
13	0.1689	-0.0188	0.0876	0.2428	0.0175	0.064	0.0209	0.0179	0.0421	0.0366	-0.0236	0.0009	0.0137	-0.0216	0.0028	0.0209	0.0183	0.0051	0.0672	0.0229	0.0279	15.4077	14.3431	31.2813
14	0.1522	-0.0134	0.0326	0.5341	-0.1943	0.1399	0.0079	0.0284	0.0328	0.0304	-0.0365	-0.0154	-0.0087	-0.0326	0.0286	0.0124	0.0054	0.001	0.0504	-0.0082	0.0263	19.9438	15.6018	37.536
15	0.1959	0.0441	0.508	0.1871	0.1551	1.7377	-0.0129	0.0157	0.0258	0.0414	-0.0063	0.0097	0.0087	-0.0371	0.0192	0.0173	-0.0031	-0.0044	0.0246	0.0025	0.0302	19.1196	6.7459	44.9114
16	0.4003	-0.0824	0.6092	0.0178	-0.0976	2.5288	-0.0362	-0.0296	-0.0529	0.0082	0.0086	0.0149	0.1094	-0.051	0.0275	0.0384	-0.0038	0.002	0.0126	0.0034	0.0286	27.8526	-25.2137	38.5039
17	0.6299	-0.3501	0.6108	0.2705	-0.3048	0.9528	0.0104	-0.0219	-0.0421	0.0044	0.0092	0.0416	0.0993	-0.0578	-0.0196	0.0226	-0.013	0.0048	0.0284	-0.0028	0.0203	20.6349	-20.6487	37.9336
18	0.3143	-0.0382	-0.1076	0.0417	0.0984	0.2353	0.0277	0.0018	-0.0067	0.0007	-0.0048	-0.0079	0.002	-0.0176	-0.0229	0.0114	-0.0145	0.0061	0.0269	-0.001	0.0484	21.9408	-15.2158	26.2737
19	0.6074	-0.2959	0.0252	0.2459	-0.1218	0.2025	-0.0114	0.0039	0.027	0.0015	0.0362	0.0109	0.0343	-0.0475	-0.0248	0.0154	-0.0128	0.0051	0.0314	-0.0047	0.0278	18.7334	-12.5448	37.7014
20	0.3189	-0.1616	0.3462	0.1497	-0.2841	1.467	-0.0106	-0.023	-0.0133	-0.0096	0.0016	0.0238	0.0424	0.0191	0.009	0.0085	-0.0044	0.0048	0.0209	-0.0121	0.032	28.4797	-19.0497	40.0557
21	0.494	-0.1188	0.8384	0.2106	-0.4967	1.9724	0.0212	0.0499	-0.0622	0.0024	-0.0193	-0.0159	0.0031	0.1053	-0.0019	0.0093	0.0092	-0.012	0.0198	-0.0019	0.0471	57.9058	-19.0354	23.8702
22	0.7728	0.0031	0.5965	0.0455	-0.1044	0.7954	0.0273	0.0418	-0.0264	-0.03	-0.0349	0.0009	0.1271	0.0924	0.0076	0.0346	0.017	0.0103	0.0294	-0.0097	0.0175	50.7616	-22.6142	22.5396
23	0.0797	-0.3095	0.2246	1.4836	-0.8342	0.6429	0.0091	0.0196	-0.0194	-0.0529	0.0232	0.1669	0.0008	0.0633	-0.0323	0.0167	-0.0036	-0.0209	0.0406	0.0213	0.0405	44.5822	-1.44	6.5063
24	0.2176	0.2655	0.015	0.3339	-0.0028	0.2814	-0.0044	-0.0073	0.0041	-0.0136	-0.0203	0.0061	0.0551	0.0164	0.0247	0.0209	0.0092	-0.0001	0.0121	-0.007	0.0432	42.6042	-23.6965	24.1362
25	0.5357	-0.299	0.8037	0.2543	-0.3798	1.4911	0.0056	0.0162	-0.0367	-0.002	-0.0026	0.0583	0.0022	0.073	-0.003	0.0076	-0.0044	0.0089	0.0206	0.0041	0.034	53.3796	-17.1432	27.5417

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 58
2	X-RAY DIFFRACTION	2	A	59 - 127
3	X-RAY DIFFRACTION	3	A	128 - 171
4	X-RAY DIFFRACTION	4	A	172 - 232
5	X-RAY DIFFRACTION	5	A	233 - 288
6	X-RAY DIFFRACTION	6	B	24 - 61
7	X-RAY DIFFRACTION	7	B	62 - 112
8	X-RAY DIFFRACTION	8	B	113 - 139
9	X-RAY DIFFRACTION	9	B	140 - 217
10	X-RAY DIFFRACTION	10	B	218 - 288
11	X-RAY DIFFRACTION	11	C	25 - 58
12	X-RAY DIFFRACTION	12	C	59 - 127
13	X-RAY DIFFRACTION	13	C	128 - 174
14	X-RAY DIFFRACTION	14	C	175 - 231
15	X-RAY DIFFRACTION	15	C	232 - 288
16	X-RAY DIFFRACTION	16	D	24 - 61
17	X-RAY DIFFRACTION	17	D	62 - 110
18	X-RAY DIFFRACTION	18	D	111 - 170
19	X-RAY DIFFRACTION	19	D	171 - 232
20	X-RAY DIFFRACTION	20	D	233 - 288
21	X-RAY DIFFRACTION	21	E	24 - 61
22	X-RAY DIFFRACTION	22	E	62 - 112
23	X-RAY DIFFRACTION	23	E	113 - 139
24	X-RAY DIFFRACTION	24	E	140 - 232
25	X-RAY DIFFRACTION	25	E	233 - 288

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