PDB-5lak: Ligand-bound structure of Cavally Virus 3CL Protease

ID or keywords:

Entry

Database: PDB / ID: 5lak

Title

Ligand-bound structure of Cavally Virus 3CL Protease

Components

3Cl Protease3C-like protease
BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

Keywords

HYDROLASE /

Protease / Mesonivirus / 3CL / peptide-bound

Function / homology

Function and homology information

3'-5'-RNA exonuclease activity /

mRNA (nucleoside-2'-O-)-methyltransferase activity / cysteine-type endopeptidase activity /

RNA-dependent RNA polymerase activity / zinc ion binding /

membrane
Similarity search - Function

Biological species

Cavally virus
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.299 Å

Authors

Kanitz, M. / Heine, A. / Diederich, W.E.

Citation

Journal: Virology / Year: 2019
Title: Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus.
Authors: Kanitz, M. / Blanck, S. / Heine, A. / Gulyaeva, A.A. / Gorbalenya, A.E. / Ziebuhr, J. / Diederich, W.E.

History

Deposition	Jun 14, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 25, 2019	Group: Derived calculations Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lak.cif.gz	636.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5lak.ent.gz	538.5 KB	Display	PDB format
PDBx/mmJSON format	5lak.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/la/5lak ftp://data.pdbj.org/pub/pdb/validation_reports/la/5lak	HTTPS FTP

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Related structure data

Related structure data	5lacSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7dpv-1 7axo-1 5fuc-2 5lac-d 5rej-1 2wct-1 4xfq-d 7lbn-1 5kxq-2 5bop-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#172 - Apr 2014 RecA and Rad51 similarity (1) #242 - Feb 2020 Coronavirus Proteases similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: 3Cl Protease

B: 3Cl Protease

C: 3Cl Protease

D: 3Cl Protease

I: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

J: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

K: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

hetero molecules

146 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3Cl Protease

B: 3Cl Protease

I: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

K: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

hetero molecules

defined by author&software
73.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: 3Cl Protease

D: 3Cl Protease

J: BEZ-TYR-TYR-ASN-ECC Peptide inhibitor

hetero molecules

defined by author&software
72.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.192, 110.150, 98.496
Angle α, β, γ (deg.)	90.00, 105.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3Cl Protease / 3C-like protease Mass: 35675.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavally virus / Gene: pp1ab, CAVV_gp1 / Plasmid: pMAL-c2-(CavV pp1a-1387-1700) / Production host: Escherichia coli (E. coli) / Variant (production host): TB1 / References: UniProt: F8RL29
#2: Protein/peptide	BEZ-TYR-TYR-ASN-ECC Peptide inhibitor Mass: 676.717 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M bicine, 20% PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979742 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2015
Radiation	Monochromator: Si with Pt coating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979742 Å / Relative weight: 1
Reflection	Resolution: 2.299→50 Å / Num. obs: 65479 / % possible obs: 99.2 % / Redundancy: 3.2 % / R_sym value: 0.07 / Net I/σ(I): 13
Reflection shell	Resolution: 2.299→2.44 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.049 / Mean I/σ(I) obs: 2.6 / R_sym value: 0.031 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LAC

5lac

Resolution: 2.299→45.333 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2296	3272	5 %	Random selection
R_work	0.2078	-	-	-
obs	0.2089	65415	99.24 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.299→45.333 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9078	0	59	179	9316

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	9360
X-RAY DIFFRACTION	f_angle_d	0.888	12755
X-RAY DIFFRACTION	f_dihedral_angle_d	11.276	3302
X-RAY DIFFRACTION	f_chiral_restr	0.037	1461
X-RAY DIFFRACTION	f_plane_restr	0.003	1701

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 (%)
2.2992-2.3335	0.2964	134	0.2944	2559	X-RAY DIFFRACTION	94
2.3335-2.3699	0.2919	141	0.2786	2662	X-RAY DIFFRACTION	100
2.3699-2.4088	0.2738	144	0.2644	2742	X-RAY DIFFRACTION	100
2.4088-2.4503	0.3042	143	0.2702	2718	X-RAY DIFFRACTION	100
2.4503-2.4949	0.3148	144	0.2682	2734	X-RAY DIFFRACTION	100
2.4949-2.5429	0.2664	140	0.264	2670	X-RAY DIFFRACTION	100
2.5429-2.5948	0.3007	143	0.2536	2718	X-RAY DIFFRACTION	100
2.5948-2.6512	0.3062	142	0.2425	2689	X-RAY DIFFRACTION	100
2.6512-2.7128	0.2843	143	0.2482	2708	X-RAY DIFFRACTION	100
2.7128-2.7807	0.2493	143	0.2404	2715	X-RAY DIFFRACTION	100
2.7807-2.8558	0.278	142	0.2427	2699	X-RAY DIFFRACTION	100
2.8558-2.9399	0.2673	142	0.2489	2699	X-RAY DIFFRACTION	100
2.9399-3.0347	0.2858	142	0.2398	2708	X-RAY DIFFRACTION	100
3.0347-3.1432	0.2994	145	0.2452	2749	X-RAY DIFFRACTION	100
3.1432-3.269	0.2384	141	0.2286	2681	X-RAY DIFFRACTION	99
3.269-3.4177	0.2396	143	0.2277	2706	X-RAY DIFFRACTION	100
3.4177-3.5978	0.2489	143	0.2243	2731	X-RAY DIFFRACTION	100
3.5978-3.8231	0.1798	143	0.1847	2704	X-RAY DIFFRACTION	100
3.8231-4.1182	0.1983	142	0.1691	2712	X-RAY DIFFRACTION	99
4.1182-4.5322	0.1631	144	0.1493	2719	X-RAY DIFFRACTION	99
4.5322-5.1873	0.1595	144	0.1538	2740	X-RAY DIFFRACTION	100
5.1873-6.5323	0.1951	143	0.1853	2718	X-RAY DIFFRACTION	99
6.5323-45.3423	0.2006	141	0.169	2662	X-RAY DIFFRACTION	95

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	2.7292	-0.5079	1.2561	2.8375	-1.2206	2.9288	-0.0763	-0.3486	-0.1805	0.2059	0.0268	-0.1044	0.2381	0.0248	0.0448	0.296	0.0591	0.0602	0.2508	0.0252	0.2443	5.9267	16.941	43.6006
2	1.8912	0.0678	0.012	2.2757	-1.7495	3.569	-0.0821	0.1292	0.0337	-0.0474	-0.0544	-0.1245	-0.0408	0.1704	0.136	0.2291	-0.02	0.0256	0.1825	-0.0196	0.2169	6.0927	33.5742	22.1262
3	5.378	4.8322	1.6705	6.2997	0.9962	1.5639	0.254	-0.0952	-0.5592	0.476	0.0228	-0.3012	0.2952	-0.1719	-0.2457	0.3184	0.0269	0.0237	0.2574	0.0459	0.3151	-14.1079	20.3882	35.7538
4	2.8011	-0.6779	-1.5669	3.2695	-0.566	1.4868	0.1317	0.1414	-0.6645	0.1115	-0.0293	0.3343	0.4741	-0.4992	-0.1132	0.4	-0.1805	-0.0572	0.5247	0.1351	0.4651	-32.3956	15.969	30.1962
5	8.8574	-4.9079	0.7954	3.0442	0.8226	5.449	0.0967	0.5597	-0.8671	-0.5256	0.0112	1.3923	0.5642	-1.3355	-0.0782	0.6187	-0.2297	-0.1847	0.9029	0.1595	0.9331	-43.0251	13.8447	25.1202
6	2.906	0.69	-0.994	2.1506	-0.7449	2.8235	-0.0816	-0.065	-0.5305	0.1713	0.2321	0.5189	0.6032	-0.6022	-0.1357	0.4412	-0.076	-0.0049	0.4686	0.1853	0.4981	-28.1899	15.2847	37.5623
7	3.9568	-1.0172	-0.4915	4.497	0.5154	3.6412	-0.251	0.2865	-0.5197	-0.3858	0.1724	0.3727	0.5673	0.0413	0.0853	0.4295	-0.028	-0.0034	0.3824	0.0719	0.3473	-14.4638	19.4444	30.494
8	2.1524	-0.1281	0.0853	2.2987	-0.3797	1.5839	-0.008	0.4225	0.484	-0.14	0.3382	0.4882	-0.27	-0.7686	-0.2701	0.3113	0.056	0.0403	0.5578	0.2147	0.4959	-26.6956	33.2487	31.2884
9	3.1577	-2.6671	-2.458	2.2662	2.2468	5.1373	0.2647	-0.6809	0.9352	1.5526	0.5005	0.5721	-0.9467	0.4092	-0.5858	0.883	0.0293	0.2314	0.3448	-0.0606	0.7102	-12.4006	53.234	41.78
10	0.9106	-0.5869	-1.1612	2.7435	0.2986	1.5983	0.3145	-0.2177	0.4589	0.4514	0.1858	0.6675	-0.8033	-0.1037	-0.4277	0.59	0.0924	0.1665	0.3406	0.002	0.6022	-14.3035	49.8246	36.5384
11	1.3211	-0.8727	0.4544	1.226	-1.9759	4.4347	-0.1349	0.0617	0.1414	0.1656	-0.0322	0.4194	-0.639	-0.4704	0.1651	0.4073	0.1123	-0.1313	0.4007	-0.1729	0.5028	3.8118	23.3955	83.4732
12	0.5475	0.3349	-0.6363	0.3045	0.2084	3.9983	-0.0263	0.0891	0.2917	-0.032	0.1582	0.0707	-0.4628	-0.4513	-0.1358	0.5975	0.1647	-0.1533	0.4457	-0.0278	0.5544	6.3992	39.3685	60.3358
13	4.7185	-0.0636	-1.3448	5.3708	-0.3723	3.4997	0.0787	0.5199	0.4822	-0.0018	0.0223	0.3605	-0.795	-0.9492	-0.0878	0.5995	0.2268	-0.1695	0.6135	-0.0207	0.6229	-0.8552	43.6204	63.9177
14	4.5128	-1.803	0.7866	2.2285	-1.861	2.8299	-0.1211	-0.241	0.5381	-0.0355	0.1218	0.2642	-0.4745	-0.5203	-0.0016	0.4291	0.1601	-0.0747	0.409	-0.0912	0.4486	2.9344	33.8849	78.1871
15	4.9369	-0.1234	0.1664	1.6753	-0.8783	2.6935	-0.1888	0.1166	0.3531	-0.3406	-0.0108	0.4168	-0.3122	-0.0926	0.1928	0.4314	0.0809	-0.1169	0.2671	-0.1068	0.3513	13.9626	29.3248	75.9914
16	6.6185	-0.1971	3.5687	2.4924	-0.8437	5.437	0.0568	0.6101	-0.2315	-0.6704	-0.0539	-0.0106	-0.1403	0.733	0.0016	0.4095	0.0566	-0.002	0.4141	0.01	0.2898	28.6446	27.3377	76.8317
17	1.8711	-0.5401	2.6903	3.2988	-3.1743	5.6963	-0.1461	-0.0089	0.458	0.3028	-0.3114	-0.1235	-0.7603	0.757	0.455	0.576	0.033	-0.1519	0.4239	-0.049	0.54	18.1352	41.9353	71.104
18	4.4576	0.1852	2.0319	3.6357	-1.5075	4.1792	0.0874	-0.1235	-0.0305	0.2849	-0.1142	-0.0275	-0.2498	0.238	0.025	0.2408	-0.0148	-0.0107	0.2946	-0.0723	0.2468	31.7189	25.808	92.8079
19	6.1752	-2.1168	4.912	8.1086	-2.8688	4.1288	0.2103	-0.1014	-0.3108	-0.4578	-0.3251	0.497	0.4805	-0.3307	0.1014	0.3539	0.0383	-0.0178	0.3761	-0.1131	0.3382	22.3653	16.9562	89.6746
20	0.1857	-0.0554	0.4063	1.1372	0.1794	0.9721	0.016	-0.6826	0.5503	0.2829	-0.0577	0.8105	-0.1451	-0.314	-0.0232	0.4528	0.1521	0.0709	0.8502	-0.2685	0.8388	-8.7383	13.1117	94.1263
21	2.6027	0.2813	-0.9003	0.3812	-0.7242	1.4939	-0.0795	-0.1744	0.2504	0.1404	-0.0489	0.8123	-0.3194	-0.3709	0.0368	0.336	0.1332	0.0095	0.5293	-0.1807	0.6916	-5.4735	11.9761	88.3088
22	4.9099	-3.9827	-0.0092	5.9273	-0.0112	2.8577	-0.2716	-0.5465	0.1431	0.3259	-0.0585	0.0887	-0.0046	-0.1889	0.3272	0.2576	-0.0176	-0.0074	0.3788	-0.106	0.4418	7.9856	1.5258	89.0523
23	3.1821	-0.3983	-1.008	2.1001	0.392	1.9412	0.0511	0.0265	0.0389	-0.2748	-0.0605	0.1175	0.0396	-0.1016	0.0119	0.2963	0.0776	-0.0694	0.2866	-0.0857	0.3307	17.0093	-0.9255	79.0077

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 155 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 156 through 305 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 24 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 25 through 53 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 54 through 69 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 70 through 124 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 125 through 140 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 141 through 230 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 231 through 252 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 253 through 305 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 20 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 21 through 69 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 70 through 93 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 94 through 124 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 125 through 182 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 183 through 201 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 202 through 219 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 220 through 287 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 288 through 305 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1 through 79 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 80 through 155 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 156 through 201 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 202 through 305 )

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