PDB-3osy: Human enterovirus 71 3C protease

ID or keywords:

Entry

Database: PDB / ID: 3osy

Title

Human enterovirus 71 3C protease

Components

3C protease

Keywords

HYDROLASE / six-beta barrel / beta-ribbon / chymotrypsin fold / Protease / RIG-1 / MAVS / CstF-64 / nucleus

Function / homology

Function and homology information

RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / cytoplasm
Similarity search - Function

Biological species

Human enterovirus 71

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9923 Å

Authors

Wang, J. / Fan, T. / Wang, M. / Cui, S.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Human Enterovirus 71 3C Protease.
Authors: Cui, S. / Wang, J. / Fan, T. / Qin, B. / Guo, L. / Lei, X. / Wang, J. / Wang, M. / Jin, Q.

History

Deposition	Sep 10, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	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_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3osy.cif.gz	378.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3osy.ent.gz	312.6 KB	Display	PDB format
PDBx/mmJSON format	3osy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3osy_validation.pdf.gz	467.3 KB	Display	wwPDB validaton report
Full document	3osy_full_validation.pdf.gz	499.9 KB	Display
Data in XML	3osy_validation.xml.gz	36.2 KB	Display
Data in CIF	3osy_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/3osy ftp://data.pdbj.org/pub/pdb/validation_reports/os/3osy	HTTPS FTP

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Related structure data

Related structure data	2vb0S S: Starting model for refinement
Similar structure data	1v3a-d 2w7q-2 3nru-6 6jfo-d 5ur4-d 7dhy-2 2bin-d 1wj1-d 6qmp-d 4z7x-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

2vb0S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (2) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: 3C protease

B: 3C protease

C: 3C protease

D: 3C protease

E: 3C protease

112 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3C protease

defined by author&software
22.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 3C protease

defined by author&software
22.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 3C protease

defined by author&software
22.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: 3C protease

defined by author&software
22.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: 3C protease

defined by author&software
22.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.288, 75.121, 125.153
Angle α, β, γ (deg.)	90.00, 90.11, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq -5:126 or resseq 129: 144 or resseq 146:181 )
2	1	1	chain B and (resseq -5:126 or resseq 129: 144 or resseq 146:181 )
3	1	1	chain C and (resseq -5:126 or resseq 129: 144 or resseq 146:181 )
4	1	1	chain D and (resseq -5:126 or resseq 129: 144 or resseq 146:181 )
5	1	1	chain E and (resseq -5:126 or resseq 129: 144 or resseq 146:181 )

#1: Protein	3C protease Mass: 22491.699 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human enterovirus 71 / Strain: Beijing2007 / Gene: 3C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: B8YLV9
Sequence details	SEQUENCING CONFIRMS RESIDUE 157 IS AN ILE. THE SEQUENCE MATCHES GENBANK ACCESSION HQ615421.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.8 %
Crystal grow	Temperature: 295 K / pH: 7.7 Details: 200mM Sodium Citrate, 20% PEG3350, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2010 / Details: BARTELS MONOCHROMATOR
Radiation	Monochromator: DOUBLE CHANNEL-CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.99→65 Å / Num. obs: 19755 / % possible obs: 93.3 % / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.99→65 Å / % possible all: 79.9

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Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
XDS	PACKAGE	data reduction
XDS	PACKAGE	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VB0

2vb0

Resolution: 2.9923→41.53 Å / SU ML: 0.46 / σ(F): 1.18 / Phase error: 28.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.259	1968	5.02 %
R_work	0.206	-	-
obs	0.209	39192	98.3 %
all	-	39192	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.55 Å² / k_sol: 0.31 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	20.4386 Å²	-0 Å²	-4.4009 Å²
2-	-	-6.3186 Å²	-0 Å²
3-	-	-	-14.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.9923→41.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7225	0	0	0	7225

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7370
X-RAY DIFFRACTION	f_angle_d	1.066	9970
X-RAY DIFFRACTION	f_dihedral_angle_d	15.512	2720
X-RAY DIFFRACTION	f_chiral_restr	0.07	1140
X-RAY DIFFRACTION	f_plane_restr	0.004	1290

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1427	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1427	X-RAY DIFFRACTION	POSITIONAL	0.051
1	3	C	1427	X-RAY DIFFRACTION	POSITIONAL	0.044
1	4	D	1427	X-RAY DIFFRACTION	POSITIONAL	0.044
1	5	E	1427	X-RAY DIFFRACTION	POSITIONAL	0.046

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 (%)
2.9923-3.0671	0.3495	118	0.2974	2187	X-RAY DIFFRACTION	82
3.0671-3.15	0.329	140	0.2847	2686	X-RAY DIFFRACTION	100
3.15-3.2426	0.3404	142	0.2539	2735	X-RAY DIFFRACTION	99
3.2426-3.3472	0.2779	140	0.2541	2639	X-RAY DIFFRACTION	100
3.3472-3.4668	0.3409	142	0.2463	2706	X-RAY DIFFRACTION	99
3.4668-3.6056	0.3259	144	0.2206	2718	X-RAY DIFFRACTION	100
3.6056-3.7695	0.2335	141	0.1966	2669	X-RAY DIFFRACTION	100
3.7695-3.9681	0.301	142	0.2026	2692	X-RAY DIFFRACTION	99
3.9681-4.2165	0.2925	144	0.217	2727	X-RAY DIFFRACTION	100
4.2165-4.5417	0.2038	143	0.1665	2699	X-RAY DIFFRACTION	100
4.5417-4.9981	0.2049	144	0.1469	2684	X-RAY DIFFRACTION	99
4.9981-5.7197	0.1984	142	0.1535	2693	X-RAY DIFFRACTION	100
5.7197-7.2001	0.2136	140	0.1706	2691	X-RAY DIFFRACTION	100
7.2001-41.5349	0.1907	146	0.1817	2698	X-RAY DIFFRACTION	99

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	0.9473	-0.2408	-0.5094	2.154	-1.2916	0.6803	-0.3099	0.0785	0.2539	-0.1146	0.2353	0.4172	-0.3318	0.129	0.0501	0.4813	-0.0588	-0.1724	0.1583	0.0414	0.2347	0.6316	12.5958	11.7981
2	1.1224	0.6118	-0.7405	0.148	-0.2653	0.523	-0.3074	0.2992	0.4066	-1.1381	0.2251	0.518	0.709	0.4491	0.0005	0.889	-0.1201	-0.0974	0.39	0.0927	0.3541	8.9715	4.9677	0.5629
3	0.749	0.2097	-0.0047	0.733	-0.5087	0.474	-0.9689	-0.0353	0.2114	-1.0977	0.6524	0.7033	-0.2175	-0.2876	-0.0008	0.6662	-0.0453	-0.105	0.4257	0.007	0.2257	6.4657	8.3315	3.2433
4	1.2701	1.4311	-0.0749	3.1557	2.3076	3.1242	-0.1747	-0.4478	-0.2554	0.5218	0.3303	-0.1954	1.0553	0.3579	0.0003	0.5791	0.1373	-0.0546	0.3599	0.0471	0.4246	15.5439	-16.4511	34.7372
5	0.4162	0.0332	-0.294	0.8917	0.3036	1.3527	-0.1121	-0.203	-0.1211	-0.6637	0.079	0.3224	-1.1372	0.5858	-0.0009	0.5177	0.1458	0.003	0.2577	0.0283	0.3269	13.4198	-4.6893	24.9779
6	2.316	0.37	1.8463	1.2525	1.7591	2.9312	-1.0585	1.7609	0.3159	-0.266	0.7262	-0.1769	-1.4952	1.0171	-0.2708	-0.0349	0.357	0.2376	-0.149	-0.1176	0.2188	14.8208	-7.8999	27.3404
7	1.8936	0.7497	0.5303	0.986	0.1883	2.3465	-0.1916	0.0724	0.1405	-0.0501	0.0558	0.0525	-0.0952	0.7843	-0.033	0.1218	-0.1223	-0.0362	0.5081	0.0149	0.3196	20.6673	15.2315	60.9052
8	0.7125	0.4159	-0.5537	0.7708	-1.3085	1.6664	-0.6971	0.1317	0.1811	-0.4164	0.3782	-0.0328	0.5898	0.7167	-0.0016	0.217	-0.0656	0.0705	0.4578	0.053	0.4036	20.2622	4.1758	53.5103
9	0.8066	0.0031	0.6542	0.416	0.2691	0.9698	0.0298	1.4034	0.0671	0.1535	-0.0571	-0.0633	0.7665	0.6343	0.0122	0.2331	-0.1045	-0.0074	0.3992	0.0027	0.2934	17.3143	6.5553	51.3904
10	1.0201	-0.5823	0.9007	1.0541	0.287	1.3691	-0.0172	-0.1656	0.0246	0.2932	-0.0616	0.2205	0.5063	-0.3181	0.0001	0.2584	-0.0554	0.1464	0.2709	0.0074	0.2831	-1.0076	-6.2237	85.3241
11	0.0846	-0.2119	0.2937	1.8557	0.5172	0.4479	0.0424	0.5751	-0.027	-0.546	-0.3946	-0.1298	-0.0404	0.8474	-0.1494	-0.1157	-0.012	0.1422	0.3882	0.1459	0.3777	8.7665	-1.8235	71.2955
12	1.2743	0.269	0.0352	1.4124	-0.1936	2.2066	0.4332	-0.0835	0.0405	-0.2452	-0.1845	-0.0965	-0.0524	0.4496	0.1473	0.17	-0.1038	0.0441	0.2199	-0.0144	0.2103	3.5501	-1.9818	77.3955
13	0.5563	-1.3597	-0.787	2.0576	-0.3043	2.6353	0.1734	-0.0015	-0.2193	0.6276	-0.3597	-0.7098	0.1723	0.4868	-0.0001	0.5134	-0.0899	-0.2158	0.3425	0.1625	0.5305	26.4439	-2.2186	111.3102
14	1.186	0.2208	-0.343	2.5925	1.569	3.3657	-0.252	0.4639	-0.1058	0.6655	-0.8527	-0.1741	0.5316	-0.5107	-0.276	0.039	0.1144	-0.0768	0.2902	0.1513	0.3209	16.7002	-0.7935	96.6606
15	0.0457	0.1648	0.0226	0.2414	0.3963	0.6553	0.3513	-0.7461	-0.0586	0.0278	-0.3274	-0.3542	0.3891	-0.2404	-0.0003	0.2385	-0.0064	-0.0154	0.3939	0.1407	0.3776	20.6663	-3.3984	103.1447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID -5:91)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 92:143)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 144:181)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID -5:95)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 96:139)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 140:181)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID -5:82)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 83:132)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 133:181)
10	X-RAY DIFFRACTION	10	(CHAIN D AND RESID -5:111)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESID 112:146)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 147:181)
13	X-RAY DIFFRACTION	13	(CHAIN E AND RESID -5:111)
14	X-RAY DIFFRACTION	14	(CHAIN E AND RESID 112:146)
15	X-RAY DIFFRACTION	15	(CHAIN E AND RESID 147:181)

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