PDB-6y9i: Structure of apo Chimpanzee Polyomavirus VP1

ID or keywords:

Entry

Database: PDB / ID: 6y9i

Title

Structure of apo Chimpanzee Polyomavirus VP1

Components

Major Capsid Protein VP1

Keywords

VIRAL PROTEIN / Major Capsid Protein / Polyomavirus

Biological species

Chimpanzee polyomavirus Bob

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Stroh, L.J. / Rustmeier, N.H. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Mbio / Year: 2020
Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family.
Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T.

History

Deposition	Mar 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 12, 2020	Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6y9i.cif.gz	304.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6y9i.ent.gz		Display	PDB format
PDBx/mmJSON format	6y9i.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6y9i_validation.pdf.gz	455.6 KB	Display	wwPDB validaton report
Full document	6y9i_full_validation.pdf.gz	464.2 KB	Display
Data in XML	6y9i_validation.xml.gz	58.7 KB	Display
Data in CIF	6y9i_validation.cif.gz	84.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y9/6y9i ftp://data.pdbj.org/pub/pdb/validation_reports/y9/6y9i	HTTPS FTP

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Related structure data

Related structure data	6y5xC 6y5yC 6y5zC 6y60C 6y61C 6y63C 6y64C 6y65C 6y66C 6y67C 6y6aC 4fmgS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y5y-1 4x13-d 4fmh-2 5cpu-d 4fmh-1 4fmi-2 5cpy-d 4fmg-3 6y67-5 6y5z-d Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

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

160 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)	63.410, 82.190, 82.660
Angle α, β, γ (deg.)	68.614, 77.361, 77.488
Int Tables number	1
Space group name H-M	P1

#1: Protein	Major Capsid Protein VP1 Mass: 31953.271 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chimpanzee polyomavirus Bob / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 947 / Source method: isolated from a natural source / Formula: H₂O
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: 2.42 Å³/Da / Density % sol: 49.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sodium acetate trihydrate, PEG 3,350, 1,5-Diaminopentane dihydrochloride

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.9→46.46 Å / Num. obs: 117709 / % possible obs: 99.4 % / Redundancy: 6.95 % / B_iso Wilson estimate: 32.2 Å² / CC_1/2: 0.997 / R_rim(I) all: 0.15 / Net I/σ(I): 9.83
Reflection shell	Resolution: 1.9→1.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 8633 / CC_1/2: 0.57 / R_rim(I) all: 0.135 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4FMG

4fmg

Resolution: 1.9→46.456 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.202 / WR_factor R_work: 0.16 / SU B: 4.034 / SU ML: 0.113 / Average fsc free: 0.8978 / Average fsc work: 0.9133 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2134	5886	5 %
R_work	0.1706	111823	-
all	0.173	-	-
obs	-	117709	99.592 %

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: 28.057 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.216 Å²	-0.601 Å²	0.382 Å²
2-	-	0.19 Å²	-0.499 Å²
3-	-	-	-0.353 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→46.456 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10524	0	10	947	11481

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	10856
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	9964
X-RAY DIFFRACTION	r_angle_refined_deg	1.57	1.645	14777
X-RAY DIFFRACTION	r_angle_other_deg	1.314	1.57	23138
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.627	5	1412
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.319	22.701	485
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14	15	1730
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.55	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1436
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	12277
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2127
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	1918
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	9686
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	5082
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4992
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	781
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.049	0.2	6
X-RAY DIFFRACTION	r_metal_ion_refined	0.024	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.254	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.254	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.22	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.278	2.895	5651
X-RAY DIFFRACTION	r_mcbond_other	2.274	2.894	5650
X-RAY DIFFRACTION	r_mcangle_it	3.283	4.321	7062
X-RAY DIFFRACTION	r_mcangle_other	3.283	4.322	7063
X-RAY DIFFRACTION	r_scbond_it	2.873	3.091	5205
X-RAY DIFFRACTION	r_scbond_other	2.873	3.091	5206
X-RAY DIFFRACTION	r_scangle_it	4.214	4.542	7715
X-RAY DIFFRACTION	r_scangle_other	4.214	4.542	7715
X-RAY DIFFRACTION	r_lrange_it	5.792	34.531	11737
X-RAY DIFFRACTION	r_lrange_other	5.734	34.237	11588

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.9-1.949	0.3	431	0.274	8183	0.276	8708	0.765	0.788	98.9205	0.256
1.949-2.003	0.288	425	0.237	8087	0.239	8576	0.827	0.859	99.2537	0.216
2.003-2.06	0.263	411	0.229	7793	0.231	8256	0.861	0.864	99.3702	0.203
2.06-2.124	0.272	400	0.207	7609	0.21	8053	0.867	0.893	99.4536	0.18
2.124-2.193	0.247	386	0.198	7338	0.2	7761	0.891	0.907	99.5233	0.172
2.193-2.27	0.244	377	0.188	7150	0.191	7553	0.898	0.911	99.6558	0.161
2.27-2.356	0.222	364	0.174	6920	0.177	7307	0.91	0.928	99.6852	0.147
2.356-2.451	0.229	347	0.172	6601	0.175	6964	0.911	0.929	99.7702	0.146
2.451-2.56	0.233	336	0.185	6377	0.187	6722	0.901	0.92	99.8661	0.158
2.56-2.685	0.249	318	0.177	6051	0.18	6386	0.902	0.929	99.7338	0.152
2.685-2.829	0.221	306	0.153	5810	0.156	6118	0.937	0.951	99.9673	0.135
2.829-3	0.206	288	0.161	5477	0.164	5775	0.941	0.949	99.8268	0.144
3-3.207	0.206	272	0.154	5160	0.157	5443	0.942	0.954	99.7979	0.143
3.207-3.462	0.179	251	0.151	4777	0.153	5032	0.956	0.962	99.9205	0.146
3.462-3.79	0.188	232	0.151	4407	0.153	4645	0.95	0.96	99.8708	0.152
3.79-4.234	0.168	212	0.139	4017	0.141	4240	0.962	0.967	99.7406	0.145
4.234-4.883	0.17	184	0.129	3502	0.131	3716	0.964	0.971	99.1927	0.139
4.883-5.963	0.196	155	0.166	2945	0.168	3110	0.952	0.954	99.6785	0.18
5.963-8.365	0.212	122	0.182	2311	0.184	2439	0.943	0.952	99.754	0.198
8.365-46.456	0.213	69	0.194	1308	0.195	1380	0.944	0.947	99.7826	0.22

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