PDB-7b6a: BK Polyomavirus VP1 pentamer core (residues 30-299)

ID or keywords:

Entry

Database: PDB / ID: 7b6a

Title

BK Polyomavirus VP1 pentamer core (residues 30-299)

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / Polyomavirus / Capsid protein

Function / homology

Function and homology information

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

Biological species

BK polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.44 Å

Authors

Osipov, E.M. / Munawar, A. / Beelen, S. / Strelkov, S.V.

Funding support

Belgium, 1items

Citation

Journal: Rsc Chem Biol / Year: 2022
Title: Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors.
Authors: Osipov, E.M. / Munawar, A.H. / Beelen, S. / Fearon, D. / Douangamath, A. / Wild, C. / Weeks, S.D. / Van Aerschot, A. / von Delft, F. / Strelkov, S.V.

History

Deposition	Dec 7, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 22, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2022	Group: Database references / Derived calculations / Category: atom_type / citation / citation_author Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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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PDBx/mmCIF format	7b6a.cif.gz	510.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b6/7b6a ftp://data.pdbj.org/pub/pdb/validation_reports/b6/7b6a	HTTPS FTP

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Related structure data

Related structure data	7b69C 7b6cC 4mj0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

AAA: Major capsid protein VP1

BBB: Major capsid protein VP1

CCC: Major capsid protein VP1

DDD: Major capsid protein VP1

EEE: 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
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	138.622, 149.719, 65.488
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-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	1	VAL	VAL	ASN	ASN	AAA	A	32 - 297	3 - 268
2	1	1	VAL	VAL	ASN	ASN	BBB	B	32 - 297	3 - 268
3	2	2	GLU	GLU	ASN	ASN	AAA	A	33 - 297	4 - 268
4	2	2	GLU	GLU	ASN	ASN	CCC	C	33 - 297	4 - 268
5	3	3	VAL	VAL	LYS	LYS	AAA	A	32 - 296	3 - 267
6	3	3	VAL	VAL	LYS	LYS	DDD	D	32 - 296	3 - 267
7	4	4	VAL	VAL	ASN	ASN	AAA	A	32 - 297	3 - 268
8	4	4	VAL	VAL	ASN	ASN	EEE	E	32 - 297	3 - 268
9	5	5	GLU	GLU	LYS	LYS	BBB	B	33 - 296	4 - 267
10	5	5	GLU	GLU	LYS	LYS	CCC	C	33 - 296	4 - 267
11	6	6	VAL	VAL	LYS	LYS	BBB	B	32 - 296	3 - 267
12	6	6	VAL	VAL	LYS	LYS	DDD	D	32 - 296	3 - 267
13	7	7	VAL	VAL	ASN	ASN	BBB	B	32 - 297	3 - 268
14	7	7	VAL	VAL	ASN	ASN	EEE	E	32 - 297	3 - 268
15	8	8	GLU	GLU	LYS	LYS	CCC	C	33 - 296	4 - 267
16	8	8	GLU	GLU	LYS	LYS	DDD	D	33 - 296	4 - 267
17	9	9	GLU	GLU	ASN	ASN	CCC	C	33 - 297	4 - 268
18	9	9	GLU	GLU	ASN	ASN	EEE	E	33 - 297	4 - 268
19	10	10	VAL	VAL	VAL	VAL	DDD	D	32 - 295	3 - 266
20	10	10	VAL	VAL	VAL	VAL	EEE	E	32 - 295	3 - 266

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

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Protein , 1 types, 5 molecules AAABBBCCCDDDEEE

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 Mass: 29720.428 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BK polyomavirus / Plasmid: pETSUK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03088

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Non-polymers , 5 types, 1566 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1523 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.21 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 10% PEG 3350, 0.2 M NaJ, 0.1 M bis-tris pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 10, 2017
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9768 Å / Relative weight: 1
Reflection	Resolution: 1.44→50 Å / Num. obs: 245801 / % possible obs: 99.9 % / Redundancy: 13.2 % / B_iso Wilson estimate: 18.5 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.029 / Net I/σ(I): 16.4
Reflection shell	Resolution: 1.44→1.49 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 24335 / CC_1/2: 0.62 / R_pim(I) all: 0.562 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4mj0

4mj0

Resolution: 1.44→50 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.602 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1858	4820	1.957 %
R_work	0.1621	241527	-
all	0.163	-	-
obs	-	245801	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 22.343 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.144 Å²	-0 Å²	-0 Å²
2-	-	-0.339 Å²	0 Å²
3-	-	-	0.484 Å²

Refinement step

Cycle: LAST / Resolution: 1.44→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10145	0	79	1523	11747

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.013	10667
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	9963
X-RAY DIFFRACTION	r_angle_refined_deg	1.851	1.648	14538
X-RAY DIFFRACTION	r_angle_other_deg	1.534	1.577	23013
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.409	5	1382
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.905	22.967	546
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.322	15	1750
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.872	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1379
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	12291
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2425
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	2033
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	10327
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	5170
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	5931
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.208	0.2	1118
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.076	0.2	6
X-RAY DIFFRACTION	r_metal_ion_refined	0.16	0.2	40
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.371	0.2	52
X-RAY DIFFRACTION	r_nbd_other	0.276	0.2	165
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.255	0.2	44
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.168	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.321	1.395	5340
X-RAY DIFFRACTION	r_mcbond_other	1.321	1.394	5339
X-RAY DIFFRACTION	r_mcangle_it	2.215	2.083	6683
X-RAY DIFFRACTION	r_mcangle_other	2.214	2.084	6684
X-RAY DIFFRACTION	r_scbond_it	1.988	1.6	5324
X-RAY DIFFRACTION	r_scbond_other	1.988	1.6	5325
X-RAY DIFFRACTION	r_scangle_it	2.996	2.315	7819
X-RAY DIFFRACTION	r_scangle_other	2.996	2.315	7820
X-RAY DIFFRACTION	r_lrange_it	6.754	18.911	12185
X-RAY DIFFRACTION	r_lrange_other	6.754	18.915	12186
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.103	0.05	7800
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.099	0.05	7924
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.099	0.05	8138
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.12	0.05	7953
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.098	0.05	7726
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.098	0.05	7744
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.085	0.05	7802
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.098	0.05	7870
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.106	0.05	7781
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.112	0.05	7893

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.10348	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.10348	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.09947	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.09947	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.09892	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.09892	0.05009
4	7	AAA	X-RAY DIFFRACTION	Local ncs	0.11959	0.05009
4	8	EEE	X-RAY DIFFRACTION	Local ncs	0.11959	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.09754	0.05009
5	10	CCC	X-RAY DIFFRACTION	Local ncs	0.09754	0.05009
6	11	BBB	X-RAY DIFFRACTION	Local ncs	0.09841	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09841	0.05009
7	13	BBB	X-RAY DIFFRACTION	Local ncs	0.08547	0.05009
7	14	EEE	X-RAY DIFFRACTION	Local ncs	0.08547	0.05009
8	15	CCC	X-RAY DIFFRACTION	Local ncs	0.09827	0.05009
8	16	DDD	X-RAY DIFFRACTION	Local ncs	0.09827	0.05009
9	17	CCC	X-RAY DIFFRACTION	Local ncs	0.10576	0.05009
9	18	EEE	X-RAY DIFFRACTION	Local ncs	0.10576	0.05009
10	19	DDD	X-RAY DIFFRACTION	Local ncs	0.11206	0.05009
10	20	EEE	X-RAY DIFFRACTION	Local ncs	0.11206	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.44-1.517	0.313	334	0.296	17286	X-RAY DIFFRACTION	99.9773
1.517-1.561	0.272	351	0.25	16799	X-RAY DIFFRACTION	100
1.561-1.609	0.241	314	0.227	16307	X-RAY DIFFRACTION	99.994
1.609-1.661	0.224	293	0.205	15818	X-RAY DIFFRACTION	99.9938
1.661-1.72	0.212	296	0.191	15383	X-RAY DIFFRACTION	100
1.72-1.785	0.191	293	0.171	14774	X-RAY DIFFRACTION	100
1.785-1.857	0.171	270	0.16	14258	X-RAY DIFFRACTION	100
1.857-1.94	0.168	269	0.149	13719	X-RAY DIFFRACTION	100
1.94-2.035	0.171	260	0.145	13066	X-RAY DIFFRACTION	99.9925
2.035-2.145	0.168	263	0.139	12489	X-RAY DIFFRACTION	100
2.145-2.275	0.18	246	0.142	11797	X-RAY DIFFRACTION	100
2.275-2.432	0.175	226	0.139	11134	X-RAY DIFFRACTION	100
2.432-2.626	0.178	223	0.151	10368	X-RAY DIFFRACTION	99.9906
2.626-2.877	0.188	204	0.16	9547	X-RAY DIFFRACTION	100
2.877-3.216	0.164	176	0.153	8679	X-RAY DIFFRACTION	100
3.216-3.713	0.164	145	0.133	7728	X-RAY DIFFRACTION	99.9873
3.713-4.546	0.144	126	0.122	6587	X-RAY DIFFRACTION	99.9851
4.546-6.422	0.198	117	0.161	5139	X-RAY DIFFRACTION	100
6.422-32	0.21	72	0.21	2965	X-RAY DIFFRACTION	99.2808

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	0.3735	-0.0642	0.0869	0.2801	0.0281	0.2704	-0.0149	0.0486	0.0705	0.0166	-0.0094	0.0581	-0.0369	0.011	0.0244	0.0085	0.0057	0.0026	0.0383	0.0254	0.131	164.7038	193.3432	17.4987
2	0.4455	-0.0776	-0.0526	0.358	-0.0263	0.3328	-0.0006	0.0648	0.1542	0.0163	0.021	-0.0849	-0.0086	0.0123	-0.0204	0.0016	-0.003	-0.0002	0.0424	0.0236	0.1647	194.1397	193.0519	18.3966
3	0.4981	0.1096	0.0544	0.4677	-0.0054	0.2498	-0.019	0.0796	-0.0031	-0.03	0.0254	-0.1145	0.0308	0.0337	-0.0063	0.0073	0.0042	0.0069	0.0395	-0.0088	0.1237	202.3044	165.9967	14.7668
4	0.2564	-0.0613	-0.0231	0.4951	0.0378	0.3208	-0.0033	0.0413	-0.0728	-0.0293	0.0153	0.0058	0.0144	-0.0221	-0.012	0.0028	-0.0033	-0.0022	0.029	-0.0129	0.1165	178.9347	148.936	13.0402
5	0.2981	-0.1298	-0.0381	0.563	0.0552	0.3353	0.0205	0.0609	-0.0732	-0.003	-0.0252	0.1818	-0.0159	-0.0568	0.0047	0.0025	0.0094	-0.0061	0.0599	0.0003	0.1728	155.1907	166.3252	15.3401

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	32 - 297
2	X-RAY DIFFRACTION	2	ALL	BBB	30 - 297
3	X-RAY DIFFRACTION	3	ALL	CCC	33 - 299
4	X-RAY DIFFRACTION	4	ALL	DDD	32 - 296
5	X-RAY DIFFRACTION	5	ALL	EEE	32 - 297

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