PDB-4lev: Structure of human cGAS

ID or keywords:

Entry

Database: PDB / ID: 4lev

Title

Structure of human cGAS

Components

Cyclic GMP-AMP synthase

Keywords

TRANSFERASE / NTase / DNA sensor

Function / homology

Function and homology information

cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.952 Å

Authors

Li, P.

Citation

Journal: Immunity / Year: 2013
Title: Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization.
Authors: Li, X. / Shu, C. / Yi, G. / Chaton, C.T. / Shelton, C.L. / Diao, J. / Zuo, X. / Kao, C.C. / Herr, A.B. / Li, P.

History

Deposition	Jun 26, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4lev.cif.gz	323.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4lev.ent.gz	275.7 KB	Display	PDB format
PDBx/mmJSON format	4lev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4lev_validation.pdf.gz	439.4 KB	Display	wwPDB validaton report
Full document	4lev_full_validation.pdf.gz	454.9 KB	Display
Data in XML	4lev_validation.xml.gz	32.9 KB	Display
Data in CIF	4lev_validation.cif.gz	48.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/4lev ftp://data.pdbj.org/pub/pdb/validation_reports/le/4lev	HTTPS FTP

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Related structure data

Related structure data	4lewC 4leyC 4lezC C: citing same article (ref.)
Similar structure data	3gyj-d 6kvi-d 4xba-d 1cc2-d 4lcm-2 3gyi-d 6eo4-2 4lcm-3 3tsj-1 4u2l-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4lewC

4leyC

4lezC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cyclic GMP-AMP synthase

B: Cyclic GMP-AMP synthase

hetero molecules

86.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cyclic GMP-AMP synthase

hetero molecules

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

2

B: Cyclic GMP-AMP synthase

hetero molecules

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

3

A: Cyclic GMP-AMP synthase

hetero molecules

B: Cyclic GMP-AMP synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	212.981, 47.715, 86.869
Angle α, β, γ (deg.)	90.00, 113.89, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / h-cGAS / Mab-21 domain-containing protein 1 Mass: 43383.184 Da / Num. of mol.: 2 / Fragment: human cGAS catalytic domain, UNP residues 157-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MB21D1, C6orf150 / Production host: Escherichia coli (E. coli) References: UniProt: Q8N884, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.33 Å³/Da / Density % sol: 47.11 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-30% Jeffamine M-600, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 153 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
Radiation	Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 1.95→38.5 Å / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 1.95→1.98 Å / % possible all: 81.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	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: 1.952→38.448 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2016	3876	3.48 %	random
R_work	0.1672	-	-	-
all	0.1689	113725	-	-
obs	0.1684	111235	97.81 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.952→38.448 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6064	0	2	451	6517

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6244
X-RAY DIFFRACTION	f_angle_d	1.338	8385
X-RAY DIFFRACTION	f_dihedral_angle_d	15.027	2419
X-RAY DIFFRACTION	f_chiral_restr	0.091	901
X-RAY DIFFRACTION	f_plane_restr	0.007	1072

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 (%)
1.9516-1.9754	0.2896	107	0.2695	3001	X-RAY DIFFRACTION	75
1.9754-2.0004	0.2739	118	0.2448	3343	X-RAY DIFFRACTION	86
2.0004-2.0267	0.2446	127	0.2377	3631	X-RAY DIFFRACTION	92
2.0267-2.0545	0.2154	137	0.2105	3742	X-RAY DIFFRACTION	97
2.0545-2.0838	0.2104	145	0.1985	3898	X-RAY DIFFRACTION	99
2.0838-2.1149	0.2237	138	0.1909	3848	X-RAY DIFFRACTION	99
2.1149-2.148	0.2428	146	0.1925	3893	X-RAY DIFFRACTION	99
2.148-2.1832	0.2402	146	0.178	3922	X-RAY DIFFRACTION	100
2.1832-2.2208	0.2423	137	0.1688	3896	X-RAY DIFFRACTION	100
2.2208-2.2612	0.2043	135	0.1659	3886	X-RAY DIFFRACTION	99
2.2612-2.3047	0.1794	151	0.1741	3909	X-RAY DIFFRACTION	99
2.3047-2.3517	0.2416	139	0.1694	3872	X-RAY DIFFRACTION	99
2.3517-2.4029	0.2143	134	0.166	3888	X-RAY DIFFRACTION	100
2.4029-2.4587	0.1942	135	0.1631	3910	X-RAY DIFFRACTION	100
2.4587-2.5202	0.2035	145	0.1608	3936	X-RAY DIFFRACTION	100
2.5202-2.5883	0.2059	138	0.1577	3879	X-RAY DIFFRACTION	100
2.5883-2.6645	0.1875	144	0.1598	3995	X-RAY DIFFRACTION	100
2.6645-2.7505	0.1946	144	0.1687	3891	X-RAY DIFFRACTION	100
2.7505-2.8487	0.213	141	0.1708	3887	X-RAY DIFFRACTION	100
2.8487-2.9628	0.1978	135	0.1709	3947	X-RAY DIFFRACTION	100
2.9628-3.0975	0.2188	144	0.1701	3899	X-RAY DIFFRACTION	100
3.0975-3.2608	0.206	136	0.1812	3835	X-RAY DIFFRACTION	100
3.2608-3.4649	0.2359	144	0.1696	3989	X-RAY DIFFRACTION	100
3.4649-3.7323	0.21	136	0.1526	3914	X-RAY DIFFRACTION	100
3.7323-4.1075	0.1702	145	0.1473	3899	X-RAY DIFFRACTION	100
4.1075-4.7009	0.1644	142	0.1423	3956	X-RAY DIFFRACTION	100
4.7009-5.9192	0.1693	139	0.1589	3864	X-RAY DIFFRACTION	99
5.9192-38.4555	0.2042	148	0.1719	3829	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	5.2527	0.0758	0.6179	4.6119	0.1918	6.2951	-0.306	-0.4836	0.8585	0.7952	-0.0708	-0.3785	-1.2722	-0.2766	0.3254	0.5521	0.0052	0.0372	0.2625	-0.0722	0.5268	155.4847	24.7763	19.1948
2	3.0437	-0.3037	-0.4556	1.6918	-1.0711	2.03	0.1161	0.263	0.322	0.0759	0.0677	0.3038	-0.028	-0.2399	-0.1942	0.3125	-0.0008	-0.0852	0.4266	-0.0237	0.3472	130.4688	11.6515	1.6862
3	2.8611	0.5688	0.7006	3.7171	-0.4163	2.4039	-0.2367	0.6864	0.1733	-0.8572	0.3016	0.2688	0.2268	-0.2594	-0.0034	0.457	-0.0755	-0.1037	0.5666	0.0166	0.3424	130.0162	10.9077	-7.7415
4	1.7447	0.2924	0.5989	1.5632	0.5042	1.6127	-0.026	0.2173	-0.1377	-0.1502	0.0858	0.0267	0.0752	0.0288	-0.0461	0.1616	-0.0156	0.0164	0.1895	-0.0182	0.146	135.0257	5.7939	16.337
5	2.6829	-0.3034	-0.4979	1.2133	-0.0288	1.5416	-0.0161	0.2882	0.0299	-0.2012	-0.0049	-0.0471	-0.0502	0.0563	0.0265	0.2366	-0.0156	0.016	0.194	-0.0076	0.1678	153.4694	6.232	13.565
6	7.6724	0.0624	1.3926	3.9039	0.5656	4.1537	0.4317	0.5141	-1.0507	0.4529	-0.2358	-0.5624	0.6455	0.6825	-0.086	0.5156	0.0296	-0.0007	0.237	0.0441	0.4798	122.0146	2.8651	53.2775
7	1.0942	0.5162	0.1483	1.4987	1.1865	1.343	0.118	0.2485	-0.1181	-0.1622	-0.0894	0.3522	0.228	-0.2043	0.0219	0.4952	0.0546	-0.1709	0.587	-0.0804	0.4626	104.7868	13.2326	27.9242
8	0.9457	0.4615	0.2755	0.329	-0.0994	0.6825	-0.3368	0.743	0.1728	-1.0464	-0.0888	0.7385	0.0091	-0.0757	0.0132	0.82	0.206	-0.2898	0.8806	-0.0143	0.6017	98.9981	29.1348	16.0314
9	1.505	0.1231	-0.5648	1.9492	-0.8901	2.1804	0.3688	0.1476	-0.2769	0.0376	-0.3527	0.869	0.2722	-0.7511	-0.0031	0.4118	-0.0695	-0.1383	0.8008	-0.1369	0.7332	94.5277	11.2075	30.3593
10	1.2746	-0.8433	0.1186	1.6265	0.1596	2.0039	0.0602	0.118	-0.021	-0.0233	-0.0934	0.2658	-0.1858	-0.3604	0.0555	0.1846	0.0476	0.0047	0.2925	0.0062	0.2583	118.8332	21.3682	31.9198
11	2.0064	-0.4722	-0.7277	1.4895	0.5212	1.8524	-0.0427	0.007	-0.2256	0.0049	-0.0628	0.1817	0.0955	-0.2035	0.086	0.1685	0.0052	0.0063	0.17	0.0005	0.1903	115.7828	18.0724	48.094
12	1.8055	-0.1265	-0.5842	1.3473	0.4378	3.0423	0.0716	0.0335	0.0055	0.0714	-0.0751	0.1139	-0.0847	-0.3312	-0.0111	0.153	0.004	0.0216	0.1675	-0.0163	0.1955	115.9591	23.4218	52.3811

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 154 through 179 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 180 through 253 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 254 through 326 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 327 through 405 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 406 through 522 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 154 through 178 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 179 through 248 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 249 through 272 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 273 through 326 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 327 through 405 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 406 through 456 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 457 through 522 )

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