PDB-4a2q: Structure of duck RIG-I tandem CARDs and helicase domain

ID or keywords:

Entry

Database: PDB / ID: 4a2q

Title

Structure of duck RIG-I tandem CARDs and helicase domain

Components

RETINOIC ACID INDUCIBLE PROTEIN I

Keywords

HYDROLASE / SUPERFAMILY 2 RNA HELICASE / ATP AND DSRNA BINDING / ANTIVIRAL SIGNALLING PATHWAY

Function / homology

Function and homology information

RNA helicase activity /

hydrolase activity /

RNA helicase /

innate immune response /

RNA binding /

ATP binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

ANAS PLATYRHYNCHOS (mallard)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Kowalinski, E. / Lunardi, T. / McCarthy, A.A. / Cusack, S.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural Basis for the Activation of Innate Immune Pattern Recognition Receptor Rig-I by Viral RNA.
Authors: Kowalinski, E. / Lunardi, T. / Mccarthy, A.A. / Louber, J. / Brunel, J. / Grigorov, B. / Gerlier, D. / Cusack, S.

History

Deposition	Sep 28, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2011	Group: Database references
Revision 1.2	Feb 8, 2012	Group: Other
Revision 1.3	Apr 3, 2019	Group: Data collection / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc / pdbx_database_status Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a2q.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4a2q.ent.gz	935.7 KB	Display	PDB format
PDBx/mmJSON format	4a2q.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/a2/4a2q ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a2q	HTTPS FTP

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Related structure data

Related structure data	4a2pSC 4a2vC 4a2wC 4a2xC 4a36C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7doc-d 7m1y-d 5zms-d 2bnx-d 5wqf-d 6gts-1 2ybr-d 3c8w-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) 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

4a2pSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (1) #56 - Aug 2004 Caspases similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #224 - Aug 2018 Legumain similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: RETINOIC ACID INDUCIBLE PROTEIN I

B: RETINOIC ACID INDUCIBLE PROTEIN I

D: RETINOIC ACID INDUCIBLE PROTEIN I

E: RETINOIC ACID INDUCIBLE PROTEIN I

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

1

A: RETINOIC ACID INDUCIBLE PROTEIN I

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

2

B: RETINOIC ACID INDUCIBLE PROTEIN I

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

3

D: RETINOIC ACID INDUCIBLE PROTEIN I

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

4

E: RETINOIC ACID INDUCIBLE PROTEIN I

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

Unit cell

Length a, b, c (Å)	314.970, 134.490, 102.260
Angle α, β, γ (deg.)	90.00, 92.17, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 94
2	1	1	1	B	1 - 94
1	1	2	1	A	246 - 457
2	1	2	1	B	246 - 457
3	1	2	1	D	246 - 457
4	1	2	1	E	246 - 457
1	1	3	1	A	611 - 707
2	1	3	1	B	611 - 707
3	1	3	1	D	611 - 707
4	1	3	1	E	611 - 707
1	2	3	1	A	730 - 743
2	2	3	1	B	730 - 743
3	2	3	1	D	730 - 743
4	2	3	1	E	730 - 743
1	1	4	1	A	471 - 602
2	1	4	1	B	471 - 602
3	1	4	1	D	471 - 602
4	1	4	1	E	471 - 602
1	1	5	1	A	750 - 790
2	1	5	1	B	750 - 790
3	1	5	1	D	750 - 790
4	1	5	1	E	750 - 790
1	1	6	1	A	95 - 186
2	1	6	1	B	95 - 186
1	1	7	1	D	2 - 94
2	1	7	1	E	2 - 94
1	1	8	1	D	95 - 186
2	1	8	1	E	95 - 186

NCS ensembles :

ID
1
2
3
4
5
6
7
8

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.996959, -0.006014, 0.07769), (-0.005947, -0.999982, -0.001097), (0.077695, 0.000631, -0.996977)	-2.10358, 64.79903, 57.16931
3	given	(-0.955674, 0.076495, 0.284315), (0.082274, 0.996574, 0.008419), (-0.282697, 0.031437, -0.958694)	-78.8286, 14.1496, 53.39284
4	given	(-0.932957, -0.072516, -0.352608), (0.082222, -0.996534, -0.012605), (-0.350472, -0.040752, 0.935686)	-55.88608, 79.8201, 2.08132

#1: Protein	RETINOIC ACID INDUCIBLE PROTEIN I / RIG-I Mass: 90733.344 Da / Num. of mol.: 4 / Fragment: TANDEM CARDS AND HELICASE DOMAIN, RESIDUES 1-794 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANAS PLATYRHYNCHOS (mallard) / Plasmid: PFASTBAC / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: D3TI84
Sequence details	ADDITIONAL GAM AT N-TERMINUS AFTER CLEAVAGE OF HIS-TAG

#1: Protein

RETINOIC ACID INDUCIBLE PROTEIN I / RIG-I

Mass: 90733.344 Da / Num. of mol.: 4 / Fragment: TANDEM CARDS AND HELICASE DOMAIN, RESIDUES 1-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ANAS PLATYRHYNCHOS (mallard) / Plasmid: PFASTBAC / Cell line (production host): High Five / Production host:

TRICHOPLUSIA NI (cabbage looper) / References: UniProt: D3TI84

Sequence details

ADDITIONAL GAM AT N-TERMINUS AFTER CLEAVAGE OF HIS-TAG

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.9 % / Description: NONE
Crystal grow	Details: 12 MG/ML PROTEIN AND 0.2 M TRI-SODIUM CITRATE, 17% PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 21, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 3.4→50 Å / Num. obs: 57366 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 7.27 % / R_merge(I) obs: 0.11 / Net I/σ(I): 15.5
Reflection shell	Resolution: 3.4→3.5 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.87 / Mean I/σ(I) obs: 2.1 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0116	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A2P

4a2p

Resolution: 3.4→157.37 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.893 / SU B: 74.197 / SU ML: 0.519 / Cross valid method: THROUGHOUT / ESU R Free: 0.608 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2764	2904	5.1 %	RANDOM
R_work	0.23879	-	-	-
obs	0.2407	54462	97.59 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 129.542 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.65 Å²	0 Å²	-1.38 Å²
2-	-	-5.58 Å²	0 Å²
3-	-	-	1.83 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→157.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21661	0	0	0	21661

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.02	22001
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	15143
X-RAY DIFFRACTION	r_angle_refined_deg	1.111	1.967	29683
X-RAY DIFFRACTION	r_angle_other_deg	0.822	3	37008
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.936	5	2662
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.961	24.62	1052
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.205	15	4184
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.295	15	153
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	3400
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	23975
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4262
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1302	tight positional	0.01	0.05
1	2	B	1302	tight positional	0.01	0.05
2	1	A	2713	tight positional	0.02	0.05
2	2	B	2713	tight positional	0.02	0.05
2	3	D	2713	tight positional	0.02	0.05
2	4	E	2713	tight positional	0.02	0.05
3	1	A	915	tight positional	0.02	0.05
3	2	B	915	tight positional	0.02	0.05
3	3	D	915	tight positional	0.02	0.05
3	4	E	915	tight positional	0.02	0.05
4	1	A	1656	tight positional	0.02	0.05
4	2	B	1656	tight positional	0.02	0.05
4	3	D	1656	tight positional	0.02	0.05
4	4	E	1656	tight positional	0.02	0.05
5	1	A	625	tight positional	0.02	0.05
5	2	B	625	tight positional	0.02	0.05
5	3	D	625	tight positional	0.02	0.05
5	4	E	625	tight positional	0.01	0.05
6	1	A	1282	tight positional	0.02	0.05
6	2	B	1282	tight positional	0.02	0.05
7	1	D	1288	tight positional	0.01	0.05
7	2	E	1288	tight positional	0.01	0.05
8	1	D	1282	tight positional	0.01	0.05
8	2	E	1282	tight positional	0.01	0.05
1	1	A	1302	tight thermal	1.92	0.5
1	2	B	1302	tight thermal	1.92	0.5
2	1	A	2713	tight thermal	5.9	0.5
2	2	B	2713	tight thermal	6.38	0.5
2	3	D	2713	tight thermal	6.34	0.5
2	4	E	2713	tight thermal	7.01	0.5
3	1	A	915	tight thermal	7.01	0.5
3	2	B	915	tight thermal	7.61	0.5
3	3	D	915	tight thermal	8.5	0.5
3	4	E	915	tight thermal	7.25	0.5
4	1	A	1656	tight thermal	4.69	0.5
4	2	B	1656	tight thermal	4.98	0.5
4	3	D	1656	tight thermal	5.65	0.5
4	4	E	1656	tight thermal	5.61	0.5
5	1	A	625	tight thermal	7	0.5
5	2	B	625	tight thermal	7.23	0.5
5	3	D	625	tight thermal	7.41	0.5
5	4	E	625	tight thermal	7.3	0.5
6	1	A	1282	tight thermal	2.12	0.5
6	2	B	1282	tight thermal	2.12	0.5
7	1	D	1288	tight thermal	6.63	0.5
7	2	E	1288	tight thermal	6.63	0.5
8	1	D	1282	tight thermal	3.38	0.5
8	2	E	1282	tight thermal	3.38	0.5

LS refinement shell

Resolution: 3.4→3.488 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.341	227	-
R_work	0.298	3986	-
obs	-	-	99.67 %

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	7.1068	0.2922	-0.8658	12.9055	2.3112	9.3067	-0.0717	0.5448	0.1529	-0.6773	0.1033	0.8231	0.7039	-0.5113	-0.0316	0.4283	-0.0003	-0.1172	0.1757	-0.0061	0.0733	-58.5058	-0.6519	-0.0783
2	6.7921	0.6184	-4.8921	11.1237	4.6456	8.6539	-0.0683	-0.2627	0.0636	0.4258	0.3022	-0.1396	1.345	0.213	-0.2339	0.4943	0.0277	-0.0928	0.1072	-0.0518	0.0393	-57.5841	8.3561	22.3843
3	3.51	-0.1114	-1.0718	9.3126	-0.7943	3.5379	-0.1185	0.3755	-0.4366	-0.3781	0.0099	-0.5333	0.2313	-0.0284	0.1086	0.2991	-0.0463	0.0203	0.3851	-0.0686	0.1225	-56.8319	-8.6016	65.8033
4	4.695	0.3605	3.3325	2.9875	-0.0103	7.8036	-0.0898	-0.1819	-0.228	0.476	0.2792	-0.1627	0.2465	0.0366	-0.1894	0.3208	0.0873	0.0962	0.2836	0.0334	0.0859	-64.3012	23.0964	43.2325
5	7.0096	0.5674	-0.0988	15.2946	2.1933	9.0129	-0.1227	-0.4377	-0.0948	0.6481	0.0504	0.8613	-0.548	-0.6367	0.0722	0.2843	0.0521	0.1332	0.1759	-0.004	0.0929	-60.2981	65.7514	52.7646
6	6.3294	-1.1993	4.7838	12.1645	5.2938	10.3963	0.1552	0.2443	-0.0204	-0.3718	0.2906	-0.1059	-1.2401	0.2036	-0.4459	0.4493	-0.0083	0.168	0.0944	-0.036	0.0765	-57.7419	56.7556	30.4246
7	3.0885	0.2324	0.764	9.1809	-0.8796	3.806	-0.1667	-0.4274	0.3665	0.5156	0.0615	-0.407	-0.2742	-0.1299	0.1052	0.3689	0.1127	-0.0122	0.4282	-0.0751	0.0785	-53.9447	73.7541	-12.8518
8	4.8896	-0.3842	-3.6295	2.927	0.1589	8.0346	-0.0538	0.1729	0.1986	-0.462	0.236	-0.1736	-0.1729	0.0474	-0.1823	0.3315	-0.1031	-0.0718	0.2706	0.0382	0.058	-63.0192	42.0446	9.1522
9	0.0949	0.56	-0.0489	5.4966	-2.8843	12.0057	0.1084	-0.1048	0.2556	0.7989	1.281	0.9816	1.4724	-2.2641	-1.3893	1.1425	-0.6334	-0.4555	2.389	0.2049	2.9767	-21.3506	13.7577	65.9435
10	1.8253	-2.8301	-1.0263	10.0439	-6.1451	12.9799	-0.2141	0.0454	-0.5323	-0.4414	0.1581	0.8741	2.7324	-1.9547	0.056	1.4816	-1.2901	-0.7911	1.6689	0.3537	2.8999	-22.592	12.0797	41.1942
11	10.2806	2.4211	0.7811	6.3686	0.9948	2.4638	1.1345	0.1685	-0.9592	0.3989	-0.4883	-0.9197	0.4013	0.4556	-0.6462	0.9998	0.2352	-0.419	0.7803	-0.4367	1.1047	-26.4693	-20.5671	-5.8381
12	1.813	1.3892	2.2769	2.2412	4.0092	8.1817	0.3877	0.1056	-0.2568	0.3323	-0.1101	-0.6995	1.1062	-0.1878	-0.2776	0.669	0.0278	-0.1879	0.7293	0.0399	2.9278	-15.6863	17.8573	16.0837
13	0.0822	-0.2611	0.5185	0.8819	-1.8431	4.3289	0.324	-0.2294	-0.05	-0.1841	0.9207	0.5563	-0.4054	-0.9553	-1.2448	2.2578	0.4298	0.4024	3.1305	0.6845	3.5368	-18.4955	51.8462	-10.477
14	1.1904	2.8511	-1.0089	7.7774	-4.084	7.8275	0.0117	0.5245	0.1681	-0.104	0.871	0.2412	-2.2733	-1.7891	-0.8827	1.5286	0.9844	0.3475	1.7289	0.7997	3.437	-21.5261	53.2981	14.1552
15	11.9159	-2.4369	0.3642	6.821	1.1403	2.2237	1.2416	-0.0495	1.2023	-0.302	-0.5261	-1.0457	-0.2982	0.5127	-0.7155	0.8041	-0.0396	0.3343	0.7126	-0.4229	1.1964	-28.7719	85.5512	61.0707
16	2.3567	-2.3933	-1.8477	3.1512	3.7971	8.202	0.3629	0.1063	0.7223	-0.3904	-0.0447	-1.0836	-1.2874	-0.4015	-0.3182	0.4823	0.0739	-0.384	0.5682	0.0444	3.0636	-16.4589	47.2751	39.621

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 94
2	X-RAY DIFFRACTION	2	A	95 - 186
3	X-RAY DIFFRACTION	3	A	245 - 466
4	X-RAY DIFFRACTION	3	A	745 - 791
5	X-RAY DIFFRACTION	4	A	467 - 744
6	X-RAY DIFFRACTION	5	B	1 - 94
7	X-RAY DIFFRACTION	6	B	95 - 186
8	X-RAY DIFFRACTION	7	B	245 - 466
9	X-RAY DIFFRACTION	7	B	745 - 792
10	X-RAY DIFFRACTION	8	B	467 - 744
11	X-RAY DIFFRACTION	9	D	2 - 94
12	X-RAY DIFFRACTION	10	D	95 - 186
13	X-RAY DIFFRACTION	11	D	245 - 466
14	X-RAY DIFFRACTION	11	D	745 - 791
15	X-RAY DIFFRACTION	12	D	467 - 744
16	X-RAY DIFFRACTION	13	E	2 - 94
17	X-RAY DIFFRACTION	14	E	95 - 186
18	X-RAY DIFFRACTION	15	E	245 - 466
19	X-RAY DIFFRACTION	15	E	745 - 791
20	X-RAY DIFFRACTION	16	E	467 - 744

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