PDB-8p61: Crystal structure of O'nyong'nyong virus capsid protease (106-256)

ID or keywords:

Entry

Database: PDB / ID: 8p61

Title

Crystal structure of O'nyong'nyong virus capsid protease (106-256)

Components

Capsid protein

Keywords

VIRUS / Capsid protease / Onyongnyong virus / Alphaviruses

Function / homology

Function and homology information

togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...
Similarity search - Function

Biological species

O'nyong-nyong virus strain Gulu

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Plewka, J. / Chykunova, Y. / Wilk, P. / Sienczyk, M. / Dubin, G. / Pyrc, K.

Funding support

Poland, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Autoinhibition of suicidal capsid protease from O'nyong'nyong virus.
Authors: Chykunova, Y. / Plewka, J. / Wilk, P. / Sienczyk, M. / Dubin, G. / Pyrc, K.

History

Deposition	May 24, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release
Revision 2.0	May 15, 2024	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: atom_site / pdbx_poly_seq_scheme ...atom_site / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / struct_conf / struct_ncs_dom_lim / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_planes.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8p61.cif.gz	241.9 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	8p61.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8p61_validation.pdf.gz	478.4 KB	Display	wwPDB validaton report
Full document	8p61_full_validation.pdf.gz	482.7 KB	Display
Data in XML	8p61_validation.xml.gz	25.7 KB	Display
Data in CIF	8p61_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p6/8p61 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p61	HTTPS FTP

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Related structure data

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	#103 - Jul 2008 Dengue Virus similarity (3) #197 - May 2016 Zika Virus similarity (3) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Capsid protein

B: Capsid protein

C: Capsid protein

D: Capsid protein

hetero molecules

68 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Capsid protein

B: Capsid protein

hetero molecules

defined by author&software
Evidence: light scattering, DLS
33.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Capsid protein

hetero molecules

D: Capsid protein

hetero molecules

defined by author&software
34.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.650, 112.130, 67.100
Angle α, β, γ (deg.)	90.000, 89.970, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	D-557- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	109 - 256	6 - 153
2	1	1	GLY	GLY	109 - 256	6 - 153
3	2	2	GLY	GLY	109 - 256	6 - 153
4	2	2	GLY	GLY	109 - 256	6 - 153
5	3	3	THR	THR	109 - 253	6 - 150
6	3	3	THR	THR	109 - 253	6 - 150
7	4	4	GLY	GLY	109 - 256	6 - 153
8	4	4	GLY	GLY	109 - 256	6 - 153
9	5	5	THR	THR	109 - 253	6 - 150
10	5	5	THR	THR	109 - 253	6 - 150
11	6	6	THR	THR	109 - 253	6 - 150
12	6	6	THR	THR	109 - 253	6 - 150

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

#1: Protein	Capsid protein / Coat protein / C Mass: 16617.910 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) O'nyong-nyong virus strain Gulu / Strain: Gulu / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22056, togavirin
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.54 Å³/Da / Density % sol: 51.52 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution ...Details: 0.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution and flash-cooled in liquid nitrogen

Crystal

Density Matthews: 2.54 Å³/Da / Density % sol: 51.52 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.46 Å / Num. obs: 51622 / % possible obs: 98.9 % / Redundancy: 1.7 % / CC_1/2: 0.961 / Net I/σ(I): 2.5
Reflection shell	Resolution: 1.9→1.94 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3314 / CC_1/2: 0.157

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→44.865 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.253 / WR_factor R_work: 0.208 / SU B: 9.62 / SU ML: 0.232 / Average fsc free: 0.8963 / Average fsc work: 0.8992 / Cross valid method: FREE R-VALUE / ESU R: 0.177 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.268	2100	4.07 %
R_work	0.2253	49497	-
all	0.227	-	-
obs	-	51597	98.868 %

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: 42.13 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.036 Å²	0 Å²	0.52 Å²
2-	-	-1.658 Å²	0 Å²
3-	-	-	4.694 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→44.865 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4514	0	84	262	4860

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4767
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	4472
X-RAY DIFFRACTION	r_angle_refined_deg	1.588	1.658	6456
X-RAY DIFFRACTION	r_angle_other_deg	0.609	1.59	10357
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.186	5	610
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.157	5	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.509	10	803
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.445	10	199
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	700
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5525
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1051
X-RAY DIFFRACTION	r_nbd_refined	0.163	0.2	814
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.161	0.2	4034
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	2254
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2615
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	290
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.007	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.108	0.2	60
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	231
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.093	0.2	33
X-RAY DIFFRACTION	r_mcbond_it	4.069	4.042	2383
X-RAY DIFFRACTION	r_mcbond_other	4.046	4.043	2383
X-RAY DIFFRACTION	r_mcangle_it	5.986	7.26	2979
X-RAY DIFFRACTION	r_mcangle_other	5.987	7.264	2980
X-RAY DIFFRACTION	r_scbond_it	5.63	4.769	2384
X-RAY DIFFRACTION	r_scbond_other	5.431	4.704	2337
X-RAY DIFFRACTION	r_scangle_it	8.667	8.417	3466
X-RAY DIFFRACTION	r_scangle_other	8.427	8.306	3395
X-RAY DIFFRACTION	r_lrange_it	11.721	51.69	5208
X-RAY DIFFRACTION	r_lrange_other	11.593	50.904	5139
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	4304
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.129	0.05	4114
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.15	0.05	3967
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.126	0.05	4155
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.149	0.05	4009
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.125	0.05	4139

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07992	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07992	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12894	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12894	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.14963	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.14963	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12616	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12616	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.14948	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.14948	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12542	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12542	0.0501

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	0.506	155	0.504	3650	0.504	3839	0.616	0.539	99.1143	0.509
1.949-2.003	0.389	153	0.422	3616	0.421	3803	0.843	0.815	99.106	0.419
2.003-2.061	0.38	145	0.387	3409	0.386	3588	0.835	0.843	99.0524	0.376
2.061-2.124	0.385	142	0.35	3340	0.352	3529	0.865	0.871	98.6682	0.329
2.124-2.193	0.358	136	0.335	3226	0.336	3432	0.882	0.893	97.9604	0.309
2.193-2.27	0.32	132	0.313	3109	0.313	3318	0.895	0.91	97.6793	0.287
2.27-2.356	0.285	130	0.28	3049	0.28	3195	0.921	0.931	99.4992	0.247
2.356-2.451	0.296	125	0.257	2959	0.258	3103	0.932	0.943	99.3877	0.221
2.451-2.56	0.29	120	0.259	2821	0.26	2959	0.934	0.947	99.3917	0.224
2.56-2.685	0.3	114	0.237	2689	0.24	2824	0.945	0.956	99.2564	0.205
2.685-2.829	0.305	108	0.218	2557	0.222	2684	0.941	0.966	99.2921	0.192
2.829-3	0.277	104	0.211	2438	0.214	2561	0.953	0.97	99.2581	0.188
3-3.206	0.26	96	0.199	2259	0.201	2409	0.961	0.975	97.7584	0.186
3.206-3.462	0.234	88	0.178	2089	0.18	2209	0.964	0.981	98.5514	0.173
3.462-3.79	0.196	84	0.154	1983	0.156	2082	0.975	0.987	99.2795	0.155
3.79-4.233	0.193	76	0.152	1774	0.154	1866	0.977	0.986	99.1425	0.155
4.233-4.881	0.213	66	0.164	1564	0.166	1642	0.974	0.985	99.2692	0.174
4.881-5.96	0.253	57	0.196	1339	0.199	1403	0.963	0.981	99.5011	0.204
5.96-8.356	0.226	43	0.197	1024	0.198	1098	0.976	0.978	97.1767	0.203
8.356-44.865	0.258	26	0.231	599	0.232	636	0.949	0.97	98.2704	0.262

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