PDB-4jcf: S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Comp...

ID or keywords:

Entry

Database: PDB / ID: 4jcf

Title

S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN /

beta-sandwich / jelly roll topology / major capsid protein / PML-associated VP1 mutation / LSTc receptor motif

Function / homology

Function and homology information

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

Biological species

JC polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 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 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jcf.cif.gz	504.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4jcf.ent.gz	416.9 KB	Display	PDB format
PDBx/mmJSON format	4jcf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4jcdC 4jceC 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3nxd-d 4x16-d 4jcd-d 4x0y-d 4x12-d 4we0-d 4x0z-d 4x11-d 4x10-d 4x13-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

C: Major capsid protein VP1

A: Major capsid protein VP1

B: 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)	149.970, 96.060, 128.220
Angle α, β, γ (deg.)	90.00, 110.36, 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	(0.443486, 0.850489, 0.282823), (-0.855099, 0.30694, 0.417843), (0.268562, -0.427149, 0.863376)	10.83471, 20.63783, -5.27882
3	given	(-0.447299, 0.514681, 0.731456), (-0.529086, -0.811653, 0.247564), (0.721104, -0.276268, 0.635362)	31.42373, 15.49269, -15.56462
4	given	(-0.440194, -0.535684, 0.720606), (0.520924, -0.806034, -0.280974), (0.731346, 0.251698, 0.633862)	33.25585, -7.95942, -16.89066
5	given	(0.449753, -0.85095, 0.271307), (0.847068, 0.310077, -0.431658), (0.283193, 0.423954, 0.86027)	13.93551, -17.62242, -7.13992

#1: Protein

Major capsid protein VP1 /

/ Major structural protein VP1

Mass: 30135.955 Da / Num. of mol.: 5 / Mutation: S268F
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: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine

Type: oligosaccharide

, Oligosaccharide

/ Class: Glycan component

/ Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine

Descriptor	Type	Program
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5NCC/3=O]/1-2-3/a4-b1_b6-c2	WURCS	PDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

#3: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL /

Glycerol

Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 838 / 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: 57.19 %
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: 2.2→47 Å / Num. all: 86277 / Num. obs: 86277 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 29.2 Å² / Net I/σ(I): 11.61
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.34 / Num. unique all: 6184 / % possible all: 96.4

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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: 2.2→44.64 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.934 / SU B: 7.96 / SU ML: 0.105 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20058	4321	5 %	RANDOM
R_work	0.16368	-	-	-
obs	0.16554	81956	99.57 %	-
all	-	86277	-	-

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: 21.401 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→44.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9952	0	80	838	10870

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	10346
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9550
X-RAY DIFFRACTION	r_angle_refined_deg	1.335	1.958	14095
X-RAY DIFFRACTION	r_angle_other_deg	0.739	3	21987
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.472	5	1311
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.611	24.261	467
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.103	15	1636
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.846	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1594
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11825
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2398
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→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.271	285	-
R_work	0.217	5882	-
obs	-	6167	96.43 %

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	0.6336	-0.3394	0.9112	0.2108	-0.3831	2.1642	-0.0417	-0.0079	0.04	0.0069	0.0278	-0.0413	-0.173	0.0041	0.0139	0.0351	-0.0221	-0.0045	0.0553	0.0188	0.0607	62.7324	15.5687	22.9889
2	0.2391	-0.0907	0.3446	0.1621	-0.0502	0.5632	-0.0195	0.0511	0.0323	-0.0029	-0.0223	-0.0029	-0.03	0.0699	0.0418	0.0222	-0.0222	0.0011	0.0669	0.0337	0.04	57.4	11.4503	17.1786
3	0.1397	-0.2251	0.0649	0.4084	-0.1966	0.2594	0.0047	0.0402	-0.0028	0.0034	-0.0509	-0.0052	-0.0284	0.0489	0.0462	0.0183	-0.0181	0.0099	0.0931	0.0202	0.0445	54.1028	3.8494	12.4229
4	0.2236	-0.091	-0.1476	0.5659	0.2836	0.5693	-0.0425	0.0864	0.0151	0.0014	-0.0269	0.0006	0.0323	0.0438	0.0694	0.0134	-0.009	0.0038	0.075	0.0142	0.0441	58.6681	0.9155	17.4731
5	0.8734	-0.0331	1.02	0.1054	0.0847	1.3508	-0.035	0.0297	0.0076	0.0049	0.0156	0.0088	-0.0331	0.0293	0.0194	0.029	-0.0145	-0.0036	0.0547	0.0228	0.0483	59.87	10.6101	25.156
6	1.8499	0.6545	1.9514	0.2603	0.7506	3.4399	-0.0423	-0.1559	0.0426	-0.0052	-0.0297	0.0382	-0.1998	-0.1221	0.072	0.0368	0.016	-0.0046	0.0327	0.0089	0.0534	41.3585	30.4525	45.6232
7	0.05	-0.0185	0.0136	0.2706	-0.3528	0.464	-0.0468	0.0503	0.0672	0.1235	-0.0117	-0.059	-0.1593	-0.0082	0.0585	0.093	-0.0227	-0.0711	0.0632	0.0621	0.0989	35.523	32.1282	24.5985
8	0.7974	0.2563	0.2879	0.1005	0.0552	0.202	0.0034	0.0158	-0.0028	0.0085	0.0165	-0.0029	0.0118	-0.0187	-0.0199	0.0454	0.02	-0.0028	0.047	0.01	0.0682	28.0838	18.3993	28.6016
9	0.3761	-0.1879	-0.0041	0.1042	-0.0636	0.8359	-0.0322	0.0058	0.0571	0.0093	0.0029	-0.02	-0.0849	0.04	0.0293	0.0538	-0.0243	-0.0167	0.0199	0.0307	0.0794	46.8085	28.5624	21.345
10	0.5	0.2085	0.4571	0.1651	0.2264	0.8474	-0.0402	0.0232	0.0445	0.0141	0.0054	0.0042	-0.0366	0.0091	0.0348	0.0345	0.0115	0.0028	0.0337	0.0037	0.0575	37.1051	23.4437	35.4164
11	0.6669	0.4551	1.443	0.4415	0.7919	3.4062	0.017	-0.0704	0.0117	0.0629	-0.009	0.0297	-0.0331	-0.2143	-0.008	0.0234	0.0268	0.0037	0.0661	-0.0102	0.0349	14.1048	5.2443	48.68
12	0.1884	-0.0373	0.395	0.3661	-0.1588	1.4263	0.0116	-0.0419	0.0212	0.0115	-0.0055	0.0412	0.0026	-0.1479	-0.0061	0.0068	0.0149	0.0056	0.0685	0.004	0.0424	13.2989	12.0657	41.1837
13	0.0894	-0.0057	0.0615	0.6329	0.047	0.0511	0.0082	-0.0311	0.0127	-0.061	-0.0117	-0.0084	-0.0059	-0.0413	0.0035	0.0162	0.0234	0.0163	0.086	0.0116	0.0582	15.9831	7.3901	29.5131
14	0.1081	0.0484	-0.0626	0.4592	-0.2695	0.3419	0.0091	0.0134	0.0491	0.016	-0.0246	-0.0161	-0.0112	-0.0689	0.0155	0.0276	0.0167	0.0059	0.0507	-0.0064	0.0647	18.9244	17.1657	37.1117
15	0.1825	0.0524	0.6196	0.2448	0.2448	2.1818	-0.0112	0.016	0.005	0.0303	-0.0046	0.0005	-0.0216	-0.002	0.0159	0.0207	0.0066	0.0107	0.0624	0.0009	0.0477	19.3197	7.2201	45.509
16	0.4394	-0.1146	1.0936	0.1222	0.0928	4.5182	0.0367	-0.063	-0.1324	-0.0151	0.0791	0.0632	0.1047	0.003	-0.1158	0.0132	-0.0253	0.0069	0.073	0.0069	0.0834	28.9483	-25.0005	40.5382
17	0.6887	-0.3941	0.6407	0.2583	-0.3275	1.2604	0.0171	0.021	-0.05	0.0071	-0.0082	0.0309	0.1385	-0.064	-0.0089	0.0288	-0.0178	0.0061	0.0247	-0.009	0.0664	20.8979	-20.2259	36.9985
18	0.368	-0.0133	-0.1035	0.0097	0.0442	0.2219	0.0216	0.0198	-0.0345	0.0045	-0.0058	0.0021	0.0233	-0.0329	-0.0158	0.0284	-0.0222	0.0064	0.0434	-0.0081	0.0776	22.6725	-14.5186	26.0316
19	0.6369	-0.3153	-0.0487	0.2331	-0.0642	0.354	0.0041	0.0082	0.0518	0.0079	0.0162	0.0076	0.0587	-0.0644	-0.0203	0.0236	-0.0177	0.0124	0.0439	-0.0019	0.063	18.3163	-12.3672	37.411
20	0.3849	-0.0728	0.389	0.0191	-0.1638	2.1202	-0.0373	-0.0093	-0.0272	0.0016	0.0053	0.0008	0	-0.0209	0.0321	0.0291	-0.0041	0.0061	0.0324	-0.0169	0.0527	28.754	-18.65	40.6465
21	0.5607	-0.1105	1.1693	0.363	-0.462	2.6802	0.0394	0.1104	-0.0527	0.006	0.0194	0.0027	0.0321	0.2083	-0.0588	0.0314	0.0099	-0.0047	0.056	-0.0129	0.0493	57.9792	-18.5316	24.5035
22	1.7539	0.1101	1.3691	0.0089	0.1032	1.562	0.016	0.169	-0.0885	0.0051	0.0044	0.0017	0.2016	0.1464	-0.0204	0.0769	0.0156	0.0036	0.0287	-0.0273	0.0573	47.2181	-24.7508	17.2268
23	0.0381	0.0468	-0.0108	0.0674	-0.0089	0.2381	0.0066	0.0097	0.013	-0.0003	0.0004	0.0358	0.0292	0.0654	-0.0069	0.035	0.0156	-0.0002	0.0562	-0.0137	0.0718	48.0376	-12.4524	20.5223
24	0.2116	0.242	0.0217	0.3245	0.0043	0.3867	0.0043	0.0044	0.0056	-0.0237	-0.0321	0.0257	0.0734	0.0126	0.0278	0.0403	0.0129	-0.0021	0.0352	-0.0143	0.068	42.2377	-23.234	23.5496
25	0.58	-0.1888	0.6915	0.2672	-0.3387	1.0521	-0.0016	0.0044	-0.01	-0.0072	-0.0325	0.0293	0.0119	0.0498	0.0341	0.0238	0.005	0.0134	0.0418	-0.012	0.053	53.8696	-16.6422	28.527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	25 - 60
2	X-RAY DIFFRACTION	2	A	61 - 127
3	X-RAY DIFFRACTION	3	A	128 - 169
4	X-RAY DIFFRACTION	4	A	170 - 232
5	X-RAY DIFFRACTION	5	A	233 - 288
6	X-RAY DIFFRACTION	6	B	24 - 48
7	X-RAY DIFFRACTION	7	B	49 - 101
8	X-RAY DIFFRACTION	8	B	102 - 148
9	X-RAY DIFFRACTION	9	B	149 - 220
10	X-RAY DIFFRACTION	10	B	221 - 288
11	X-RAY DIFFRACTION	11	C	25 - 58
12	X-RAY DIFFRACTION	12	C	59 - 110
13	X-RAY DIFFRACTION	13	C	111 - 168
14	X-RAY DIFFRACTION	14	C	169 - 231
15	X-RAY DIFFRACTION	15	C	232 - 288
16	X-RAY DIFFRACTION	16	D	24 - 58
17	X-RAY DIFFRACTION	17	D	59 - 110
18	X-RAY DIFFRACTION	18	D	111 - 168
19	X-RAY DIFFRACTION	19	D	169 - 232
20	X-RAY DIFFRACTION	20	D	233 - 288
21	X-RAY DIFFRACTION	21	E	24 - 61
22	X-RAY DIFFRACTION	22	E	62 - 90
23	X-RAY DIFFRACTION	23	E	99 - 160
24	X-RAY DIFFRACTION	24	E	161 - 231
25	X-RAY DIFFRACTION	25	E	232 - 288

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