PDB-4wdy: JC Polyomavirus VP1 five-fold pore mutant N221Q

ID or keywords:

Entry

Database: PDB / ID: 4wdy

Title

JC Polyomavirus VP1 five-fold pore mutant N221Q

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / beta-sandwich / jelly-roll / viral major capsid protein / five-fold pore

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

Stroh, L.J. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2015
Title: Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins.
Authors: Nelson, C.D. / Stroh, L.J. / Gee, G.V. / O'Hara, B.A. / Stehle, T. / Atwood, W.J.

History

Deposition	Sep 9, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wdy.cif.gz	511.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4wdy.ent.gz	423.1 KB	Display	PDB format
PDBx/mmJSON format	4wdy.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/wd/4wdy ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wdy	HTTPS FTP

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Related structure data

Related structure data	4wdzC 4we0C 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4jce-d 3nxg-d 4x0y-d 4x11-d 4wdz-d 4x16-d 4x0z-d 4jcd-d 4mj1-d 4x14-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)	149.710, 95.790, 128.510
Angle α, β, γ (deg.)	90.00, 110.38, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	VAL	VAL	A	A	26 - 29	9 - 12
2	1	VAL	VAL	VAL	VAL	B	B	26 - 29	9 - 12
3	1	VAL	VAL	VAL	VAL	C	C	26 - 29	9 - 12
4	1	VAL	VAL	VAL	VAL	D	D	26 - 29	9 - 12
5	1	VAL	VAL	VAL	VAL	E	E	26 - 29	9 - 12
1	2	THR	THR	ASP	ASP	A	A	31 - 51	14 - 34
2	2	THR	THR	ASP	ASP	B	B	31 - 51	14 - 34
3	2	THR	THR	ASP	ASP	C	C	31 - 51	14 - 34
4	2	THR	THR	ASP	ASP	D	D	31 - 51	14 - 34
5	2	THR	THR	ASP	ASP	E	E	31 - 51	14 - 34
1	3	HIS	HIS	PHE	PHE	A	A	53 - 57	36 - 40
2	3	HIS	HIS	PHE	PHE	B	B	53 - 57	36 - 40
3	3	HIS	HIS	PHE	PHE	C	C	53 - 57	36 - 40
4	3	HIS	HIS	PHE	PHE	D	D	53 - 57	36 - 40
5	3	HIS	HIS	PHE	PHE	E	E	53 - 57	36 - 40
1	4	PRO	PRO	ILE	ILE	A	A	78 - 85	61 - 68
2	4	PRO	PRO	ILE	ILE	B	B	78 - 85	61 - 68
3	4	PRO	PRO	ILE	ILE	C	C	78 - 85	61 - 68
4	4	PRO	PRO	ILE	ILE	D	D	78 - 85	61 - 68
5	4	PRO	PRO	ILE	ILE	E	E	78 - 85	61 - 68
1	5	MET	MET	VAL	VAL	A	A	101 - 111	84 - 94
2	5	MET	MET	VAL	VAL	B	B	101 - 111	84 - 94
3	5	MET	MET	VAL	VAL	C	C	101 - 111	84 - 94
4	5	MET	MET	VAL	VAL	D	D	101 - 111	84 - 94
5	5	MET	MET	VAL	VAL	E	E	101 - 111	84 - 94
1	6	ALA	ALA	THR	THR	A	A	126 - 162	109 - 145
2	6	ALA	ALA	THR	THR	B	B	126 - 162	109 - 145
3	6	ALA	ALA	THR	THR	C	C	126 - 162	109 - 145
4	6	ALA	ALA	THR	THR	D	D	126 - 162	109 - 145
5	6	ALA	ALA	THR	THR	E	E	126 - 162	109 - 145
1	7	ASN	ASN	LEU	LEU	A	A	173 - 189	156 - 172
2	7	ASN	ASN	LEU	LEU	B	B	173 - 189	156 - 172
3	7	ASN	ASN	LEU	LEU	C	C	173 - 189	156 - 172
4	7	ASN	ASN	LEU	LEU	D	D	173 - 189	156 - 172
5	7	ASN	ASN	LEU	LEU	E	E	173 - 189	156 - 172
1	8	ALA	ALA	THR	THR	A	A	194 - 205	177 - 188
2	8	ALA	ALA	THR	THR	B	B	194 - 205	177 - 188
3	8	ALA	ALA	THR	THR	C	C	194 - 205	177 - 188
4	8	ALA	ALA	THR	THR	D	D	194 - 205	177 - 188
5	8	ALA	ALA	THR	THR	E	E	194 - 205	177 - 188
1	9	PHE	PHE	VAL	VAL	A	A	240 - 287	223 - 270
2	9	PHE	PHE	VAL	VAL	B	B	240 - 287	223 - 270
3	9	PHE	PHE	VAL	VAL	C	C	240 - 287	223 - 270
4	9	PHE	PHE	VAL	VAL	D	D	240 - 287	223 - 270
5	9	PHE	PHE	VAL	VAL	E	E	240 - 287	223 - 270
1	10	ILE	ILE	SER	SER	A	A	112 - 122	95 - 105
2	10	ILE	ILE	SER	SER	B	B	112 - 122	95 - 105
3	10	ILE	ILE	SER	SER	C	C	112 - 122	95 - 105
4	10	ILE	ILE	SER	SER	D	D	112 - 122	95 - 105
5	10	ILE	ILE	SER	SER	E	E	112 - 122	95 - 105

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.44078, 0.853573, 0.277716), (-0.856622, 0.30758, 0.414237), (0.268161, -0.420485, 0.866765)	11.5878, 20.15611, -5.78389
3	given	(-0.449023, 0.513278, 0.731385), (-0.52777, -0.812853, 0.246434), (0.720998, -0.275348, 0.635882)	31.77968, 14.10822, -15.77693
4	given	(-0.441147, -0.53469, 0.72076), (0.519328, -0.807097, -0.280879), (0.731906, 0.250402, 0.633728)	32.80217, -9.30723, -16.69683
5	given	(0.448894, -0.8519, 0.269741), (0.848029, 0.310984, -0.42911), (0.281674, 0.421373, 0.862035)	13.28813, -18.20094, -6.79227

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 / Mad-1 Mass: 30089.889 Da / Num. of mol.: 5 / Fragment: UNP Residues 23-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) JC polyomavirus / Plasmid: plasmid / Details (production host): pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.87 Å³/Da / Density % sol: 57.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2010
Radiation	Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 131987 / % possible obs: 98.1 % / Redundancy: 4.1 % / B_iso Wilson estimate: 31.9 Å² / Net I/σ(I): 9.4
Reflection shell	Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.7 / % possible all: 83.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.94 / SU B: 7.856 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22917	6536	5 %	RANDOM
R_work	0.19076	-	-	-
obs	0.19271	123517	97.13 %	-

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: 31.057 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	0 Å²	0.39 Å²
2-	-	-0.71 Å²	-0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10012	0	46	724	10782

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	10332
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9618
X-RAY DIFFRACTION	r_angle_refined_deg	1.315	1.956	14038
X-RAY DIFFRACTION	r_angle_other_deg	0.748	3	22160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.426	5	1299
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.989	24.277	470
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.728	15	1675
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.419	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	1576
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11781
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2377
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	2.467	6.243	5172
X-RAY DIFFRACTION	r_mcbond_other	2.466	6.242	5171
X-RAY DIFFRACTION	r_mcangle_it	2.929	8.386	6452
X-RAY DIFFRACTION	r_mcangle_other	2.93	8.387	6453
X-RAY DIFFRACTION	r_scbond_it	3.812	7.322	5160
X-RAY DIFFRACTION	r_scbond_other	3.81	7.322	5160
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.008	9.489	7578
X-RAY DIFFRACTION	r_long_range_B_refined	6.661	17.115	11703
X-RAY DIFFRACTION	r_long_range_B_other	6.661	17.118	11704
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: 2619 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.24	0.5
B	medium positional	0.29	0.5
C	medium positional	0.26	0.5
D	medium positional	0.24	0.5
E	medium positional	0.22	0.5
A	medium thermal	1.95	2
B	medium thermal	1.76	2
C	medium thermal	1.84	2
D	medium thermal	1.72	2
E	medium thermal	1.7	2

LS refinement shell

Resolution: 1.9→1.949 Å / Num. reflection R_free: 326 / Num. reflection R_work: 6513

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	0.8024	-0.0091	0.5949	0.7743	-0.281	1.6275	-0.1149	0.042	0.0593	0.0856	0.0392	-0.0929	-0.1747	0.2513	0.0756	0.0423	0.0128	-0.0294	0.1475	0.0147	0.1139	60.3216	11.6743	18.5709
2	0.4538	-0.2246	0.1186	0.7045	0.0765	0.6065	-0.0196	0.044	-0.0109	0.0014	-0.0093	-0.0337	-0.0094	0.0539	0.0289	0.0236	-0.0217	-0.0377	0.1136	0.0235	0.0727	57.9486	5.346	18.5124
3	4.8994	0.17	4.6386	0.5822	0.3166	5.8795	-0.1535	0.0046	0.1414	0.0703	-0.0443	-0.0544	-0.1477	0.1194	0.1977	0.0253	-0.0212	-0.0099	0.051	0.0239	0.0538	58.9104	12.0185	23.9885
4	8.561	0.115	3.7309	1.5796	-0.3965	2.8519	0.0064	-0.3201	-0.1287	0.1062	0.0149	-0.0608	-0.2422	-0.0715	-0.0213	0.2608	-0.003	-0.0301	0.2268	-0.019	0.1982	44.4985	30.2207	52.0871
5	0.8948	0.0462	-0.0852	0.1817	-0.2205	0.7606	-0.0311	-0.0115	0.0889	0.0176	0.0134	0.0113	-0.1345	-0.0415	0.0177	0.0612	0.0106	-0.0533	0.0831	0.0009	0.1051	37.9547	25.0359	25.2184
6	2.4584	0.931	2.616	1.1313	1.1132	4.5704	-0.0336	-0.0956	0.0242	0.0673	-0.0065	-0.0568	-0.11	0.0628	0.0401	0.046	0.0265	-0.0105	0.081	0.0117	0.0717	38.5788	25.7316	35.6832
7	4.3573	2.4627	3.655	3.1474	2.2833	6.9479	0.2151	-0.0818	-0.1733	0.5154	0.0131	-0.0704	0.3085	-0.0083	-0.2282	0.1701	0.0348	-0.0298	0.2151	-0.0119	0.146	21.8362	5.5234	63.0153
8	0.4229	-0.025	0.23	0.976	-0.0322	0.4809	-0.005	-0.0331	0.0416	0.0186	0.0101	0.0591	-0.0423	-0.1049	-0.0051	0.0188	0.015	-0.0292	0.1376	0.0008	0.087	15.5393	11.0154	35.6934
9	1.215	0.2105	1.4545	0.8834	0.922	5.449	0.0169	-0.0926	0.0392	0.1109	0.0015	-0.0519	-0.0685	0.0225	-0.0185	0.0275	0.0024	-0.0187	0.081	0.0236	0.1027	19.4384	6.8557	46.0681
10	0.4902	-0.4596	1.0008	2.4846	3.3024	12.363	-0.0389	-0.0522	-0.079	0.1532	0.0216	-0.0366	0.1634	0.2875	0.0174	0.1276	-0.0426	-0.0098	0.2358	0.0543	0.1926	35.2234	-24.8561	55.9389
11	0.8569	-0.0874	-0.1395	0.3815	0.2262	0.7049	0.0066	-0.0131	-0.0252	-0.0001	0.014	0.0532	0.0715	-0.0633	-0.0206	0.0277	-0.0154	-0.044	0.096	0.0055	0.0904	21.011	-16.8357	33.3221
12	0.98	-0.2056	1.0513	0.7709	-0.569	6.0697	-0.0327	-0.1432	-0.0156	0.0962	0.053	0.0368	-0.0985	-0.0229	-0.0202	0.0244	-0.0004	-0.0271	0.0809	-0.0013	0.0955	28.1834	-19.7098	41.3185
13	1.8495	0.1328	0.5283	0.8755	-1.4777	10.1513	-0.0474	-0.1081	-0.0487	0.2113	-0.0454	-0.1883	-0.2716	0.3768	0.0928	0.1408	0.0467	-0.0178	0.1433	-0.0223	0.1708	65.1853	-20.6591	41.5457
14	0.5444	0.2372	0.1321	0.3768	-0.0827	0.7337	0.0166	0.0454	-0.0491	-0.0509	-0.007	0.0061	0.0575	0.051	-0.0096	0.0237	0.014	-0.0353	0.0903	-0.0148	0.0905	46.1784	-20.0166	20.8973
15	1.8696	-0.7464	2.2374	1.1453	-1.3036	4.3903	-0.0457	-0.0337	0.0161	0.0586	-0.0302	-0.011	-0.0189	0.0283	0.0759	0.0087	-0.0027	-0.0119	0.0643	-0.0254	0.076	53.6794	-17.9231	27.1634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 68
2	X-RAY DIFFRACTION	2	A	69 - 263
3	X-RAY DIFFRACTION	3	A	264 - 288
4	X-RAY DIFFRACTION	4	B	24 - 42
5	X-RAY DIFFRACTION	5	B	43 - 237
6	X-RAY DIFFRACTION	6	B	238 - 288
7	X-RAY DIFFRACTION	7	C	25 - 42
8	X-RAY DIFFRACTION	8	C	43 - 232
9	X-RAY DIFFRACTION	9	C	233 - 289
10	X-RAY DIFFRACTION	10	D	24 - 42
11	X-RAY DIFFRACTION	11	D	43 - 236
12	X-RAY DIFFRACTION	12	D	237 - 289
13	X-RAY DIFFRACTION	13	E	24 - 42
14	X-RAY DIFFRACTION	14	E	43 - 238
15	X-RAY DIFFRACTION	15	E	239 - 288

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About Yorodumi

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Yorodumi