PDB-6j52: Crystal structure of CARD-only protein in frog virus 3

ID or keywords:

Entry

Database: PDB / ID: 6j52

Title

Crystal structure of CARD-only protein in frog virus 3

Components

Caspase recruitment domain-only protein

Keywords

APOPTOSIS / Death domain superfamily / Caspase recruitment domain / CARD-only protein / Domain swapping

Function / homology

CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / regulation of apoptotic process / Putative interleukin-1 beta convertase

Function and homology information

Biological species

Frog virus 3

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.504 Å

Authors

Park, H.H. / Kwon, S.

Funding support

Korea, Republic Of, 1items

Citation

Journal: J. Struct. Biol. / Year: 2019
Title: Structural transformation-mediated dimerization of caspase recruitment domain revealed by the crystal structure of CARD-only protein in frog virus 3.
Authors: Kim, C.M. / Ha, H.J. / Kwon, S. / Jeong, J.H. / Lee, S.H. / Kim, Y.G. / Lee, C.S. / Lee, J.H. / Park, H.H.

History

Deposition	Jan 10, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 22, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6j52.cif.gz	151.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6j52_validation.pdf.gz	442.6 KB	Display	wwPDB validaton report
Full document	6j52_full_validation.pdf.gz	442.9 KB	Display
Data in XML	6j52_validation.xml.gz	13.2 KB	Display
Data in CIF	6j52_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/6j52 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j52	HTTPS FTP

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Related structure data

Related structure data	1dgnS S: Starting model for refinement
Similar structure data	1i54-d 1lfm-d 1i55-d 1czp-d 6kty-d 3m9k-d 4bkg-1 2alg-d 132 4tlq-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	#177 - Sep 2014 Apoptosomes similarity (4) #56 - Aug 2004 Caspases similarity (4) #224 - Aug 2018 Legumain similarity (4) #122 - Feb 2010 Enhanceosome similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: Caspase recruitment domain-only protein

B: Caspase recruitment domain-only protein

C: Caspase recruitment domain-only protein

D: Caspase recruitment domain-only protein

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

1

A: Caspase recruitment domain-only protein

B: Caspase recruitment domain-only protein

defined by author&software
Evidence: gel filtration
23.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Caspase recruitment domain-only protein

D: Caspase recruitment domain-only protein

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

Unit cell

Length a, b, c (Å)	46.657, 60.500, 78.836
Angle α, β, γ (deg.)	90.00, 89.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Caspase recruitment domain-only protein Mass: 11568.339 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Frog virus 3 / Gene: orf64R, RUK13gorf64R, SSMEgorf64R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8SPG9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.4 Å³/Da / Density % sol: 48.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.5M NaCl, 0.1M imidazole pH 8.0, 10%(w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 15193 / % possible obs: 99.8 % / Redundancy: 3.7 % / R_sym value: 0.108 / Net I/σ(I): 38.02
Reflection shell	Resolution: 2.5→2.54 Å / Num. unique obs: 780 / R_sym value: 0.216

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3139: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DGN

1dgn

Resolution: 2.504→40.098 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.28

	R_factor	Num. reflection	% reflection
R_free	0.2363	1513	9.98 %
R_work	0.1682	-	-
obs	0.1748	15157	98.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.504→40.098 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2851	0	0	13	2864

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2863
X-RAY DIFFRACTION	f_angle_d	0.849	3828
X-RAY DIFFRACTION	f_dihedral_angle_d	6.759	1794
X-RAY DIFFRACTION	f_chiral_restr	0.043	451
X-RAY DIFFRACTION	f_plane_restr	0.004	502

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 (%)
2.5039-2.5847	0.2725	131	0.1824	1140	X-RAY DIFFRACTION	91
2.5847-2.677	0.2841	136	0.1852	1249	X-RAY DIFFRACTION	99
2.677-2.7842	0.2747	138	0.1904	1230	X-RAY DIFFRACTION	100
2.7842-2.9109	0.2775	144	0.1906	1241	X-RAY DIFFRACTION	100
2.9109-3.0643	0.2933	141	0.1901	1243	X-RAY DIFFRACTION	100
3.0643-3.2562	0.2566	136	0.192	1227	X-RAY DIFFRACTION	100
3.2562-3.5075	0.281	137	0.1745	1266	X-RAY DIFFRACTION	100
3.5075-3.8602	0.2411	139	0.1581	1246	X-RAY DIFFRACTION	100
3.8602-4.4181	0.1791	129	0.1429	1260	X-RAY DIFFRACTION	100
4.4181-5.564	0.1878	135	0.1414	1271	X-RAY DIFFRACTION	100
5.564-40.1031	0.1954	147	0.1643	1271	X-RAY DIFFRACTION	98

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	0.125	-0.035	0.0335	0.0488	0.0852	0.2217	0.1171	0.16	0.0079	0.0069	0.0266	-0.015	0.02	0.2054	0.0131	0.1599	0.0212	0.0323	0.1085	0.0089	0.1478	34.934	18.8235	30.804
2	0.1874	0.0355	0.0836	0.1908	-0.0169	0.7245	0.0934	0.0061	-0.0394	0.0225	0.1896	0.0274	-0.0067	-0.0968	0.1747	0.0805	0.0285	-0.0127	0.0203	-0.0067	0.1111	12.8576	13.6154	13.3829
3	0.0162	-0.0053	-0.0085	0.0076	0.002	0.0249	0.1215	0.0654	0.2015	-0.1233	-0.0958	-0.136	-0.0777	-0.0158	0.0001	0.1933	0.0267	0.069	0.154	0.0424	0.1991	9.1853	25.4887	5.6125
4	0.1329	-0.0698	-0.0487	0.0721	0.0006	0.0663	0.1743	0.1519	-0.0239	-0.0113	-0.0537	-0.0251	-0.1965	-0.1266	0.0056	0.1543	-0.006	0.0281	0.1342	0.0053	0.1683	9.3168	20.9077	10.5186
5	0.0037	-0.0075	0.003	0.0237	0.0134	0.0153	-0.0184	-0.0469	-0.0494	-0.0709	0.0203	-0.0435	0.0399	-0.0312	0.0141	-0.0089	0.0298	0.0742	0.5758	0.2156	0.2405	10.6304	14.6896	24.0295
6	0.0126	-0.0115	-0.0081	0.1483	-0.0106	0.0104	0.0316	0.1017	-0.1009	-0.0193	0.0997	-0.1305	0.0304	0.0174	0.1705	-0.0947	-0.111	-0.1139	0.0192	-0.0551	0.0786	32.2134	13.5429	28.5802
7	0.0014	-0.0079	-0.0121	0.0469	0.0728	0.0953	-0.0645	0.0161	0.0635	0.1448	0.1638	0.0813	-0.1304	0.0431	0.0429	0.1603	0.0079	0.0504	0.1484	-0.032	0.165	35.3266	21.9063	39.4267
8	0.0661	-0.0021	0.0561	0.0038	0.0237	0.0946	-0.0152	-0.0942	0.0384	-0.0816	0.0846	-0.1957	0.0118	-0.0422	0.0049	0.1854	-0.0027	0.006	0.1075	-0.0567	0.1555	59.7704	-3.5494	4.6105
9	0.064	-0.0284	0.032	0.0426	-0.0109	0.0805	-0.0322	0.0106	-0.0152	-0.1712	0.0422	-0.0038	-0.1143	-0.0184	0.0046	0.088	0.0144	-0.1012	0.3809	-0.1405	0.1179	63.1284	-4.1412	18.2689
10	0.034	0.0166	-0.0062	0.0267	0.0257	0.0217	0.028	-0.0721	-0.1068	-0.0366	0.0826	0.0192	-0.0261	-0.0858	0.003	0.1259	0.0411	-0.0081	0.1305	0.0354	0.1398	36.1017	-6.0098	29.7521
11	0.004	0.0081	-0.0108	0.0238	-0.0263	0.0356	0.021	-0.0011	-0.0059	-0.0102	-0.0136	-0.0093	0.0484	0.0306	-0.0138	0.1245	0.0154	-0.0261	0.1279	-0.0011	0.1003	36.3359	-10.0067	39.7068
12	0.0218	-0.0289	0.0294	0.1077	-0.0865	0.0822	-0.1128	-0.0613	0.0942	0.4326	-0.0609	0.039	-0.0534	-0.0232	-0.0235	0.14	-0.0106	0.0115	0.0953	0.0317	0.1187	36.9217	-3.2249	34.7261
13	0.0291	-0.0029	-0.0054	0.0348	0.0185	0.0164	0.1149	0.2525	0.0333	-0.089	0.1297	0.0472	0.0695	-0.0182	0.0051	0.1194	0.0273	-0.036	0.2469	0.021	0.1334	34.3442	-8.9421	19.9458
14	0.008	0.0005	0.0035	0.0019	0.0042	0.0075	0.0005	-0.0369	0.0463	0.0353	0.0374	-0.0051	-0.1669	-0.0337	-0.0001	0.1483	0.0393	-0.0111	0.0911	-0.0143	0.0853	57.698	2.0296	10.588
15	0.056	-0.0218	-0.0425	0.0111	0.0246	0.0394	0.0396	0.0912	0.0419	-0.1516	0.0256	-0.0868	0.0888	0.0582	0.0633	0.166	-0.0956	-0.022	0.1744	-0.0521	0.1855	61.4358	-6.7723	0.1517

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 94 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 39 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 40 through 51 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 52 through 67 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 68 through 94 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 1 through 34 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 35 through 51 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 52 through 89 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 90 through 94 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 21 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 22 through 49 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 50 through 67 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 68 through 93 )

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