PDB-4k8v: Structure of cyclic GMP-AMP Synthase (cGAS)

ID or keywords:

Entry

Database: PDB / ID: 4k8v

Title

Structure of cyclic GMP-AMP Synthase (cGAS)

Components

Cyclic GMP-AMP synthase

Keywords

TRANSFERASE / nucleotidyltransferase / DNA

Function / homology

Function and homology information

regulation of immunoglobulin production / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / regulation of type I interferon production / poly-ADP-D-ribose modification-dependent protein binding / regulation of T cell activation / paracrine signaling / negative regulation of DNA repair / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Gao, P. / Wu, Y. / Patel, D.J.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2013
Title: Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.
Authors: Gao, P. / Ascano, M. / Wu, Y. / Barchet, W. / Gaffney, B.L. / Zillinger, T. / Serganov, A.A. / Liu, Y. / Jones, R.A. / Hartmann, G. / Tuschl, T. / Patel, D.J.

History

Deposition	Apr 18, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 28, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4k8v.cif.gz	620.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4k8v.ent.gz	512.7 KB	Display	PDB format
PDBx/mmJSON format	4k8v.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/k8/4k8v ftp://data.pdbj.org/pub/pdb/validation_reports/k8/4k8v	HTTPS FTP

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Related structure data

Related structure data	4k96C 4k97C 4k98C 4k99C 4k9aC 4k9bC C: citing same article (ref.)
Similar structure data	4km5-d 5vdw-1 5u7x-d 6nao-1 4lew-2 3nrn-d 3g7w-d 6enl-d 4o69-d 1ckm-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

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	#23 - Nov 2001 DNA similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

C: Cyclic GMP-AMP synthase

A: Cyclic GMP-AMP synthase

B: Cyclic GMP-AMP synthase

D: Cyclic GMP-AMP synthase

hetero molecules

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

1

C: Cyclic GMP-AMP synthase

hetero molecules

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

2

A: Cyclic GMP-AMP synthase

hetero molecules

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

3

B: Cyclic GMP-AMP synthase

hetero molecules

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

4

D: Cyclic GMP-AMP synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.563, 84.147, 124.716
Angle α, β, γ (deg.)	90.00, 92.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / m-cGAS / Mab-21 domain-containing protein 1 Mass: 42512.121 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP residues 147-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mb21d1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8C6L5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1357 / 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: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1 M HEPES, 0.1 M MgAc2, 20% PEG3350, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 120932 / Num. obs: 118611 / % possible obs: 98.08 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2→2.07 Å / % possible all: 98.6

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Processing

Software

Name	Version	Classification
CBASS		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2→44.07 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 20.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.208	5939	5.01 %
R_work	0.175	-	-
obs	0.177	118611	98.1 %
all	-	120932	-

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→44.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11957	0	4	1357	13318

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	12217
X-RAY DIFFRACTION	f_angle_d	1.207	16402
X-RAY DIFFRACTION	f_dihedral_angle_d	16.047	4768
X-RAY DIFFRACTION	f_chiral_restr	0.085	1760
X-RAY DIFFRACTION	f_plane_restr	0.005	2081

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 (%)
1.9999-2.0226	0.2499	178	0.205	3112	X-RAY DIFFRACTION	82
2.0226-2.0464	0.2768	178	0.2003	3407	X-RAY DIFFRACTION	88
2.0464-2.0713	0.2629	188	0.1945	3526	X-RAY DIFFRACTION	94
2.0713-2.0976	0.2242	186	0.1945	3684	X-RAY DIFFRACTION	96
2.0976-2.1252	0.2619	192	0.189	3732	X-RAY DIFFRACTION	98
2.1252-2.1543	0.2426	210	0.1833	3769	X-RAY DIFFRACTION	98
2.1543-2.1851	0.1938	201	0.1783	3723	X-RAY DIFFRACTION	99
2.1851-2.2177	0.2234	186	0.1791	3797	X-RAY DIFFRACTION	99
2.2177-2.2523	0.2293	201	0.1786	3718	X-RAY DIFFRACTION	99
2.2523-2.2892	0.227	185	0.1776	3820	X-RAY DIFFRACTION	99
2.2892-2.3287	0.2292	208	0.1838	3744	X-RAY DIFFRACTION	99
2.3287-2.3711	0.2234	218	0.1813	3745	X-RAY DIFFRACTION	99
2.3711-2.4167	0.2304	198	0.176	3822	X-RAY DIFFRACTION	99
2.4167-2.466	0.2189	208	0.1854	3805	X-RAY DIFFRACTION	99
2.466-2.5196	0.24	207	0.1863	3737	X-RAY DIFFRACTION	99
2.5196-2.5782	0.2251	183	0.1861	3816	X-RAY DIFFRACTION	99
2.5782-2.6427	0.244	191	0.1893	3806	X-RAY DIFFRACTION	99
2.6427-2.7141	0.2147	197	0.1832	3812	X-RAY DIFFRACTION	99
2.7141-2.794	0.2017	209	0.1845	3813	X-RAY DIFFRACTION	100
2.794-2.8841	0.2056	183	0.1838	3807	X-RAY DIFFRACTION	100
2.8841-2.9872	0.2322	225	0.1834	3779	X-RAY DIFFRACTION	100
2.9872-3.1068	0.2262	195	0.1788	3837	X-RAY DIFFRACTION	100
3.1068-3.2481	0.2284	199	0.1845	3815	X-RAY DIFFRACTION	100
3.2481-3.4193	0.2243	205	0.1722	3810	X-RAY DIFFRACTION	100
3.4193-3.6334	0.1858	214	0.1666	3828	X-RAY DIFFRACTION	100
3.6334-3.9138	0.1799	187	0.1554	3842	X-RAY DIFFRACTION	100
3.9138-4.3074	0.1649	234	0.1542	3850	X-RAY DIFFRACTION	100
4.3074-4.93	0.1651	175	0.1476	3857	X-RAY DIFFRACTION	100
4.93-6.2085	0.2036	205	0.1799	3900	X-RAY DIFFRACTION	100
6.2085-44.077	0.186	193	0.1814	3959	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	0.2946	-0.0219	0.0117	0.2046	-0.0285	0.0796	-0.1431	0.208	0.1549	0.1636	0.212	0.0007	-0.1083	-0.0053	0.0511	0.2727	0.1447	0.016	-0.0792	-0.026	0.1181	-45.5103	4.9721	-59.1802
2	0.1931	0.1586	-0.1727	0.2765	-0.0473	0.2153	0.0188	-0.0462	-0.0223	0.0816	0.0458	0.0763	-0.0606	-0.0613	0.0121	0.1845	0.0462	-0.0078	0.1017	0.0237	0.0905	-44.1812	-9.1554	-46.7697
3	0.0674	0.0102	-0.0149	0.0342	0.0045	0.1628	0.02	0.0117	-0.0473	0.0483	-0.0244	-0.0879	0.0121	-0.0284	0.0008	0.1218	0.0015	-0.0297	0.0804	0.032	0.1444	-29.0566	-9.0022	-56.788
4	0.2338	-0.1539	0.1032	0.2679	-0.0345	0.4227	-0.003	0.078	0.0457	-0.0438	-0.0027	-0.0329	0.1043	-0.0384	-0.0143	0.1119	-0.0112	0.0296	0.0848	0.0188	0.1109	-35.4763	-6.2035	-76.0703
5	0.0407	-0.0222	0.0041	0.1031	0.0747	0.051	-0.018	-0.0257	-0.1155	0.0205	-0.0294	0.0398	0.074	0.1383	-0.0001	0.179	-0.0064	0.0349	0.116	-0.0193	0.2021	-25.4518	-1.3387	-118.4373
6	0.1239	-0.0358	0.0429	0.0927	0.0974	0.1334	-0.1398	0.0441	-0.02	0.0148	0.1232	-0.0652	0.0184	-0.0344	-0.0004	0.1566	-0.0393	0.0214	0.0968	0.0307	0.1415	-25.6602	18.6833	-123.0919
7	0.117	-0.1043	-0.0882	0.1185	0.0316	0.1327	-0.1066	0.1738	-0.0276	-0.1584	0.0863	0.0634	-0.0197	0.058	-0.0027	0.1879	-0.039	-0.0416	0.1249	0.0187	0.1565	-28.6356	15.9955	-133.6588
8	0.0738	0.0267	-0.0629	0.1251	-0.0315	0.1348	-0.0294	-0.0173	0.1067	-0.0321	0.0325	0.0706	-0.0492	0.0097	0.015	0.0922	-0.012	-0.0334	0.0871	0.0092	0.1055	-23.5079	23.582	-113.7206
9	0.1876	0.1634	-0.2143	0.2367	-0.2018	0.1867	-0.0606	-0.0291	-0.1679	-0.029	0.0954	-0.0747	-0.0227	-0.0626	0.0197	0.0515	0.0042	-0.0238	0.1466	0.0323	0.015	-29.8902	8.9932	-100.4902
10	0.0791	0.0718	-0.1001	0.0597	-0.081	0.1625	0.0189	0.1751	0.1254	0.1442	0.1251	0.0853	-0.0893	-0.3356	0.0093	0.0063	0.0748	-0.0183	0.2214	0.0749	0.0898	-41.4764	14.1627	-103.1109
11	0.1029	-0.0621	0.0303	-0.0093	-0.0141	0.0066	0.0362	-0.0618	0.3049	-0.16	-0.0902	-0.0951	-0.3391	-0.1788	-0.0072	0.436	0.0753	0.0079	0.3061	0.0193	0.3188	-74.8703	30.2123	-105.9559
12	0.1047	-0.0231	-0.06	0.0398	-0.0145	0.0353	0.0759	0.2099	-0.1536	0.0088	0.0517	0.2386	-0.0435	0.1275	0.004	0.2073	0.0441	-0.0259	0.2432	-0.0303	0.1819	-70.7486	9.4164	-120.1589
13	0.2248	-0.1082	0.1138	0.103	-0.078	0.0784	0.1095	0.1736	0.1201	-0.1763	-0.0763	-0.1263	-0.302	0.2155	0.0131	0.3758	-0.1013	0.0886	0.242	0.0286	0.2303	-63.0378	25.9077	-118.4661
14	0.316	0.111	0.043	0.234	0.1463	0.39	-0.0008	-0.0786	-0.0155	0.0358	-0.0023	-0.053	0.0276	0.0663	-0.0455	0.0443	0.0129	-0.0175	0.177	-0.0076	0.0957	-74.9995	12.7786	-96.0306
15	0.0717	0.0189	0.0462	0.015	0.0129	0.0319	0.1784	0.0151	-0.1376	0.1961	-0.0132	-0.1657	0.2138	-0.066	0.0285	0.3654	-0.033	-0.0924	0.1859	0.0865	0.2683	3.6142	6.5013	-48.3318
16	0.0127	0.0031	0.0029	0.0214	-0.0159	0.0078	0.0098	0.0063	0.0127	0.0424	-0.0955	-0.1595	0.0511	0.0423	0.0001	0.7984	-0.2518	0.1063	0.8233	0.019	0.6437	-4.6459	12.7635	-41.8532
17	0.1163	0.0699	0.0673	0.4227	-0.0012	0.0978	0.3938	-0.5245	0.2897	0.3994	-0.4177	0.5257	-0.0534	-0.0586	0.0413	0.4753	-0.2709	0.3212	0.3474	-0.2278	0.0909	-10.4814	21.8376	-39.8444
18	0.5434	-0.0143	-0.0415	0.2943	-0.0342	0.093	0.0366	0.1032	0.3168	0.1048	0.0258	0.1568	0.0299	0.077	0.0303	0.1056	-0.027	0.0115	0.0932	-0.0185	0.2369	0.5435	23.2205	-62.924

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 146 through 210 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 211 through 314 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 315 through 376 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 377 through 507 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 146 through 184 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 185 through 239 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 314 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 315 through 376 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 377 through 461 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 462 through 507 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 146 through 210 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 211 through 248 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 249 through 314 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 315 through 507 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 146 through 184 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 185 through 210 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 211 through 376 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 377 through 507 )

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