PDB-4jce: L54F Variant of JC Polyomavirus Major Capsid Protein VP1

ID or keywords:

Entry

Database: PDB / ID: 4jce

Title

L54F 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: 1.9 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	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	4jce.cif.gz	522.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4jce.ent.gz	433.4 KB	Display	PDB format
PDBx/mmJSON format	4jce.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jce_validation.pdf.gz	480.2 KB	Display	wwPDB validaton report
Full document	4jce_full_validation.pdf.gz	488.9 KB	Display
Data in XML	4jce_validation.xml.gz	59.4 KB	Display
Data in CIF	4jce_validation.cif.gz	87.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jc/4jce ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jce	HTTPS FTP

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Related structure data

Related structure data	4jcdC 4jcfC 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4wdy-d 3nxg-d 4x0y-d 4x16-d 4x11-d 4we0-d 4wdz-d 4mj1-d 4jcd-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

152 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)	149.430, 95.710, 128.800
Angle α, β, γ (deg.)	90.00, 110.27, 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	(0.447589, 0.848348, 0.28279), (-0.850283, 0.305818, 0.428363), (0.276919, -0.432182, 0.858216)	-4.49305, 32.43981, 2.5568
3	given	(-0.442987, 0.52249, 0.728537), (-0.527047, -0.809142, 0.259828), (0.725248, -0.268873, 0.633816)	21.60205, 47.22795, -10.62033
4	given	(-0.451808, -0.52801, 0.719079), (0.523043, -0.80975, -0.265953), (0.7227, 0.25595, 0.642023)	42.71313, 23.98443, -20.9105
5	given	(0.439712, -0.857593, 0.266812), (0.85306, 0.305853, -0.42278), (0.280968, 0.413508, 0.866065)	29.63776, -5.31313, -14.30158

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 Mass: 30109.877 Da / Num. of mol.: 5 / Mutation: L54F 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.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1161 / 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: 2.87 Å³/Da / Density % sol: 57.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 0.2 M KSCN, 12% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING 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: 1.9→47 Å / Num. all: 132607 / Num. obs: 132607 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / B_iso Wilson estimate: 26 Å² / Net I/σ(I): 15.14
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.55 / Num. unique all: 9546 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REMAQ		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: 1.9→44.53 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.95 / SU B: 4.521 / SU ML: 0.068 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18487	6673	5 %	RANDOM
R_work	0.14917	-	-	-
obs	0.15093	125934	99.35 %	-
all	-	132607	-	-

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: 20.481 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→44.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9967	0	68	1161	11196

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	10653
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9867
X-RAY DIFFRACTION	r_angle_refined_deg	1.415	1.953	14566
X-RAY DIFFRACTION	r_angle_other_deg	0.774	3	22800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.544	5	1410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.662	24.388	490
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.487	15	1723
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.628	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	1638
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	12331
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2501
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: 1.9→1.951 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.245	473	-
R_work	0.206	9046	-
obs	-	9516	96.92 %

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	1.4583	0.1238	1.2217	0.0216	0.0296	1.5306	-0.0956	-0.0476	0.1427	0.0217	-0.0022	0.0155	-0.2843	-0.0303	0.0978	0.1045	0.0073	-0.0285	0.0077	-0.0162	0.0642	36.329	48.9166	39.8713
2	0.1135	-0.0896	0.2141	0.1616	-0.4003	1.0093	-0.1043	0.0422	0.1055	0.0807	-0.0127	-0.0583	-0.2145	-0.0097	0.117	0.1074	-0.0149	-0.0752	0.0388	0.0562	0.1107	38.2754	49.8965	25.562
3	0.4831	0.2205	0.2224	0.14	0.0933	0.1272	-0.0324	0.0083	-0.0052	-0.0187	0.0365	-0.0142	-0.0471	-0.0162	-0.0041	0.0535	0.0089	-0.008	0.0424	0.0138	0.0584	27.9751	36.2588	28.7831
4	0.5322	-0.1477	-0.1159	0.0435	0.0151	0.6052	-0.0239	0.0246	0.0984	0.0053	-0.0128	-0.0394	-0.0724	0.0231	0.0367	0.0631	-0.0214	-0.0163	0.02	0.0366	0.088	46.709	46.3938	21.3863
5	0.3726	0.1819	0.1969	0.1013	0.1267	0.514	-0.0281	-0.0173	0.0315	-0.0031	-0.0134	-0.0062	-0.0585	-0.0486	0.0415	0.0504	0.0141	-0.0194	0.0125	0.0087	0.0702	37.0772	41.3024	35.8676
6	0.8441	0.2173	1.4057	0.6344	0.3055	2.356	-0.0181	-0.1484	0.003	0.1025	0.0128	0.0856	-0.0492	-0.2766	0.0052	0.0246	0.0279	0.0135	0.0948	-0.0139	0.0329	14.6315	23.509	50.623
7	0.4254	-0.2854	0.5319	0.235	-0.3431	0.7047	-0.0805	-0.1027	0.0613	0.0362	0.0222	0.0067	-0.1054	-0.1913	0.0583	0.0196	0.0413	-0.021	0.1345	-0.0202	0.0844	10.3023	31.323	38.3182
8	0.1535	-0.0375	0.1444	0.2885	0.2606	0.4797	0.0118	0.0114	-0.0112	-0.0028	0.0094	-0.0019	-0.0136	-0.0104	-0.0212	0.0322	0.0111	0.0025	0.0592	-0.0046	0.054	18.4122	18.4878	34.3589
9	0.2225	0.0188	-0.0201	0.414	-0.2237	0.259	-0.0043	0.0208	0.0589	0.0394	-0.0045	-0.0173	-0.0265	-0.0703	0.0088	0.036	0.0236	0.0015	0.0555	-0.0004	0.0587	17.5903	36.3566	35.9753
10	0.1367	0.0365	0.4503	0.2464	0.1573	1.5588	-0.001	-0.005	0.0051	0.0353	0.0142	-0.0139	-0.0043	-0.0653	-0.0133	0.0294	0.0132	0.0061	0.0501	-0.0007	0.0548	19.3275	25.1151	46.093
11	0.5417	-0.0947	0.9902	0.0947	0.24	4.0511	-0.013	-0.0593	-0.1183	0.023	0.0319	0.057	0.1325	-0.0355	-0.0189	0.0605	-0.0217	0.0063	0.0296	0.0185	0.058	29.3626	-7.4256	42.5957
12	0.4795	-0.1662	0.4321	0.1041	-0.1536	0.8393	0.0264	-0.0236	-0.039	0.0028	-0.0124	0.0394	0.0889	-0.0618	-0.014	0.0236	-0.0267	0.0051	0.0352	-0.0026	0.0701	21.0304	-2.7926	37.0851
13	0.357	0.0081	-0.1099	0.0286	0.0421	0.1215	0.0074	0.0392	-0.0115	0.0065	0.001	0.01	0.023	-0.0292	-0.0085	0.0345	-0.0192	-0.0037	0.0462	0.0041	0.0775	22.4876	3.4582	26.1615
14	0.4613	-0.21	0.0578	0.2402	-0.0719	0.236	0.0025	-0.0285	0.0219	-0.0073	0.0273	0.0251	0.0517	-0.0465	-0.0297	0.0176	-0.0171	0.0105	0.0459	-0.0014	0.0671	18.1587	5.554	37.8218
15	0.3798	-0.1185	0.3926	0.0448	-0.1891	1.4584	0.0016	-0.0246	-0.0251	-0.0044	0.0168	0.0159	0.0192	-0.0158	-0.0184	0.0349	-0.0128	0.0098	0.0358	0.0012	0.0609	28.651	-0.8301	41.296
16	0.5416	0.004	1.0031	0.2574	-0.5702	3.2082	0.0288	0.0673	-0.0575	-0.0072	-0.0364	-0.0434	0.0383	0.172	0.0076	0.031	0.0276	0.0056	0.0517	-0.0135	0.0378	59.7691	-1.1841	27.8006
17	0.4882	0.0835	0.4247	0.0591	0.0162	0.6932	-0.0067	0.0444	-0.0159	-0.0261	-0.0317	0.0048	0.0857	0.0799	0.0384	0.0472	0.0207	0.0074	0.0444	-0.0232	0.0455	50.507	-3.914	21.8898
18	0.0813	0.1176	-0.0384	0.1948	-0.0316	0.2095	-0.0227	0.0184	-0.0095	-0.0443	0.0048	0.0118	0.0411	0.0315	0.0178	0.0474	0.0147	-0.0026	0.0509	-0.0198	0.0598	43.2301	3.7786	15.665
19	0.4828	0.1988	0.0883	0.184	-0.0786	0.2012	0.0161	0.016	-0.0317	-0.0127	-0.0307	0.0144	0.0429	0.0304	0.0146	0.0481	0.0069	0.0123	0.019	-0.0203	0.0681	42.5694	-4.3832	25.3012
20	0.4739	-0.1371	0.6882	0.1506	-0.2985	1.2171	-0.0092	0.0251	-0.0377	-0.0028	-0.0013	0.0135	-0.0161	0.0456	0.0105	0.0327	0.0117	0.0124	0.043	-0.0047	0.0544	53.6043	1.0725	28.7026
21	1.0914	-0.477	1.3165	0.2924	-0.3854	2.0563	-0.0255	0.0674	0.0883	-0.0201	0.0088	-0.0734	-0.1117	0.1431	0.0167	0.0343	-0.0416	-0.0158	0.0651	0.0356	0.0655	64.0978	33.5094	25.5183
22	0.6293	0.0437	0.6762	0.2618	0.3328	1.0474	0.0105	0.1585	0.0676	-0.0079	-0.0222	-0.0561	-0.0018	0.1474	0.0117	0.0356	-0.0287	0.0015	0.0877	0.039	0.0339	61.8177	26.152	15.2499
23	0.4392	-0.1687	0.0335	0.1258	-0.0938	0.1205	0.0093	0.035	-0.0205	0.0011	-0.0003	0.005	-0.0206	-0.0064	-0.009	0.051	-0.0158	-0.0081	0.0491	0.0239	0.0583	44.0453	32.3123	17.0138
24	0.0929	-0.0949	0.1092	0.7155	0.1193	0.3004	-0.0088	0.0741	0.0085	-0.0201	-0.032	-0.0537	0.0165	0.0843	0.0407	0.0188	-0.0128	0.0253	0.0839	0.0076	0.0439	61.6904	15.9769	13.7565
25	0.3461	0.0322	0.3343	0.1569	0.1359	0.4017	-0.0155	0.0353	0.0285	0.0007	-0.0069	-0.0141	-0.0288	0.0331	0.0224	0.0369	-0.0197	-0.0042	0.0373	0.0284	0.0589	57.1265	28.6341	25.7651

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 55
2	X-RAY DIFFRACTION	2	A	56 - 101
3	X-RAY DIFFRACTION	3	A	102 - 148
4	X-RAY DIFFRACTION	4	A	149 - 220
5	X-RAY DIFFRACTION	5	A	221 - 288
6	X-RAY DIFFRACTION	6	B	24 - 55
7	X-RAY DIFFRACTION	7	B	56 - 101
8	X-RAY DIFFRACTION	8	B	102 - 151
9	X-RAY DIFFRACTION	9	B	152 - 231
10	X-RAY DIFFRACTION	10	B	232 - 288
11	X-RAY DIFFRACTION	11	C	25 - 55
12	X-RAY DIFFRACTION	12	C	56 - 111
13	X-RAY DIFFRACTION	13	C	112 - 168
14	X-RAY DIFFRACTION	14	C	169 - 232
15	X-RAY DIFFRACTION	15	C	233 - 288
16	X-RAY DIFFRACTION	16	D	24 - 55
17	X-RAY DIFFRACTION	17	D	56 - 111
18	X-RAY DIFFRACTION	18	D	112 - 168
19	X-RAY DIFFRACTION	19	D	169 - 232
20	X-RAY DIFFRACTION	20	D	233 - 288
21	X-RAY DIFFRACTION	21	E	24 - 55
22	X-RAY DIFFRACTION	22	E	56 - 106
23	X-RAY DIFFRACTION	23	E	107 - 148
24	X-RAY DIFFRACTION	24	E	149 - 220
25	X-RAY DIFFRACTION	25	E	221 - 288

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