PDB-5n6i: Crystal structure of mouse cGAS in complex with 39 bp DNA

ID or keywords:

Entry

Database: PDB / ID: 5n6i

Title

Crystal structure of mouse cGAS in complex with 39 bp DNA

Components

Cyclic GMP-AMP synthase
DNA (36-MER)
DNA (37-MER)

Keywords

TRANSFERASE / nucleotidyltransferase / cyclic GMP-AMP synthase / cGAS / DNA-binding / activator DNA / pattern recognition receptor / innate immune response / viral DNA recognition

Function / homology

Function and homology information

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

Biological species

Mus musculus (house mouse)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.6 Å

Authors

Andreeva, L. / Kostrewa, D. / Hopfner, K.-P.

Funding support

Germany, 2items

Citation

Journal: Nature / Year: 2017
Title: cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein-DNA ladders.
Authors: Andreeva, L. / Hiller, B. / Kostrewa, D. / Lassig, C. / de Oliveira Mann, C.C. / Jan Drexler, D. / Maiser, A. / Gaidt, M. / Leonhardt, H. / Hornung, V. / Hopfner, K.P.

History

Deposition	Feb 15, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Oct 4, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.5	Jan 17, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5n6i.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	5n6i_validation.pdf.gz	516.3 KB	Display	wwPDB validaton report
Full document	5n6i_full_validation.pdf.gz	549.7 KB	Display
Data in XML	5n6i_validation.xml.gz	77.5 KB	Display
Data in CIF	5n6i_validation.cif.gz	105.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n6/5n6i ftp://data.pdbj.org/pub/pdb/validation_reports/n6/5n6i	HTTPS FTP

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Related structure data

Related structure data	4leyS S: Starting model for refinement
Similar structure data	107 8296 6iqq-d 5497 5168 6n7l-d 6o1o-d 3ean-d 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Cyclic GMP-AMP synthase

B: Cyclic GMP-AMP synthase

C: Cyclic GMP-AMP synthase

D: Cyclic GMP-AMP synthase

E: Cyclic GMP-AMP synthase

F: Cyclic GMP-AMP synthase

G: DNA (37-MER)

H: DNA (36-MER)

I: DNA (37-MER)

J: DNA (36-MER)

K: DNA (37-MER)

L: DNA (36-MER)

M: DNA (37-MER)

N: DNA (36-MER)

hetero molecules

357 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	168.530, 122.940, 179.980
Angle α, β, γ (deg.)	90.00, 96.37, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	ASP	ASP	A	A	149 - 505	12 - 368
2	1	LYS	LYS	ASP	ASP	B	B	149 - 505	12 - 368
1	2	LYS	LYS	ASP	ASP	A	A	149 - 505	12 - 368
2	2	LYS	LYS	ASP	ASP	C	C	149 - 505	12 - 368
1	3	LYS	LYS	ASP	ASP	A	A	149 - 505	12 - 368
2	3	LYS	LYS	ASP	ASP	D	D	149 - 505	12 - 368
1	4	LYS	LYS	ASP	ASP	A	A	149 - 505	12 - 368
2	4	LYS	LYS	ASP	ASP	E	E	149 - 505	12 - 368
1	5	LYS	LYS	ASP	ASP	A	A	149 - 505	12 - 368
2	5	LYS	LYS	ASP	ASP	F	F	149 - 505	12 - 368
1	6	LYS	LYS	ASP	ASP	B	B	149 - 505	12 - 368
2	6	LYS	LYS	ASP	ASP	C	C	149 - 505	12 - 368
1	7	LYS	LYS	ASP	ASP	B	B	149 - 505	12 - 368
2	7	LYS	LYS	ASP	ASP	D	D	149 - 505	12 - 368
1	8	LYS	LYS	ASP	ASP	B	B	149 - 505	12 - 368
2	8	LYS	LYS	ASP	ASP	E	E	149 - 505	12 - 368
1	9	LYS	LYS	ASP	ASP	B	B	149 - 505	12 - 368
2	9	LYS	LYS	ASP	ASP	F	F	149 - 505	12 - 368
1	10	LYS	LYS	ASP	ASP	C	C	149 - 505	12 - 368
2	10	LYS	LYS	ASP	ASP	D	D	149 - 505	12 - 368
1	11	LYS	LYS	ASP	ASP	C	C	149 - 505	12 - 368
2	11	LYS	LYS	ASP	ASP	E	E	149 - 505	12 - 368
1	12	LYS	LYS	ASP	ASP	C	C	149 - 505	12 - 368
2	12	LYS	LYS	ASP	ASP	F	F	149 - 505	12 - 368
1	13	LYS	LYS	ASP	ASP	D	D	149 - 505	12 - 368
2	13	LYS	LYS	ASP	ASP	E	E	149 - 505	12 - 368
1	14	LYS	LYS	ASP	ASP	D	D	149 - 505	12 - 368
2	14	LYS	LYS	ASP	ASP	F	F	149 - 505	12 - 368
1	15	LYS	LYS	ASP	ASP	E	E	149 - 505	12 - 368
2	15	LYS	LYS	ASP	ASP	F	F	149 - 505	12 - 368
1	16	DG	DG	DA	DA	G	G	2 - 36	2 - 36
2	16	DG	DG	DA	DA	I	I	2 - 36	2 - 36
1	17	DG	DG	DG	DG	G	G	20 - 35	20 - 35
2	17	DG	DG	DG	DG	K	K	20 - 35	20 - 35
1	18	DG	DG	DG	DG	G	G	20 - 35	20 - 35
2	18	DG	DG	DG	DG	M	M	20 - 35	20 - 35
1	19	DA	DA	DC	DC	H	H	3 - 38	3 - 38
2	19	DA	DA	DC	DC	J	J	3 - 38	3 - 38
1	20	DT	DT	DT	DT	H	H	4 - 19	4 - 19
2	20	DT	DT	DT	DT	L	L	4 - 19	4 - 19
1	21	DT	DT	DT	DT	H	H	4 - 19	4 - 19
2	21	DT	DT	DT	DT	N	N	4 - 19	4 - 19
1	22	DG	DG	DG	DG	I	I	20 - 35	20 - 35
2	22	DG	DG	DG	DG	K	K	20 - 35	20 - 35
1	23	DG	DG	DG	DG	I	I	20 - 35	20 - 35
2	23	DG	DG	DG	DG	M	M	20 - 35	20 - 35
1	24	DT	DT	DT	DT	J	J	4 - 19	4 - 19
2	24	DT	DT	DT	DT	L	L	4 - 19	4 - 19
1	25	DT	DT	DT	DT	J	J	4 - 19	4 - 19
2	25	DT	DT	DT	DT	N	N	4 - 19	4 - 19
1	26	DG	DG	DA	DA	K	K	20 - 36	20 - 36
2	26	DG	DG	DA	DA	M	M	20 - 36	20 - 36
1	27	DT	DT	DC	DC	L	L	4 - 20	4 - 20
2	27	DT	DT	DC	DC	N	N	4 - 20	4 - 20

NCS ensembles :

#1: Protein	Cyclic GMP-AMP synthase / m-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1 Mass: 43401.180 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: DNA-binding and catalytic domain, Mab21 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mb21d1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: DNA chain	DNA (37-MER) Mass: 11987.729 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Nucleotids 1 and 39 were not visible in the electron density. Source: (synth.) synthetic construct (others)
#3: DNA chain	DNA (36-MER) Mass: 12014.771 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Nucleotids 1, 2 and 39 were not visible in the electron density. Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 52.68 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris pH 8, 0.2M ammonium citrate pH 7, 27,5% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99988 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99988 Å / Relative weight: 1
Reflection	Resolution: 3.6→47 Å / Num. obs: 41980 / % possible obs: 99 % / Redundancy: 5.07 % / Net I/σ(I): 9.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
STARANISO		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4LEY

4ley

Resolution: 3.6→47 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.935 / SU B: 141.768 / SU ML: 0.787 / Cross valid method: THROUGHOUT / ESU R Free: 0.971 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25631	1402	4.9 %	RANDOM
R_work	0.20388	-	-	-
obs	0.20646	26998	66.88 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 191.455 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.75 Å²	-0 Å²	1.58 Å²
2-	-	-3.02 Å²	-0 Å²
3-	-	-	0.89 Å²

Refinement step

Cycle: 1 / Resolution: 3.6→47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17712	4365	6	0	22083

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number	Weight
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.018	23255
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	19761
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.789	31850
X-RAY DIFFRACTION	r_angle_other_deg	1.136	3.001	46164
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.823	5.498	3260
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.261	24.056	858
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.642	15	3600
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.261	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.163	0.218	3451
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	22047
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	4728
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	4.018		8562	17.31
X-RAY DIFFRACTION	r_mcbond_other	4.016		8561	17.31
X-RAY DIFFRACTION	r_mcangle_it	6.797		10692	29.219
X-RAY DIFFRACTION	r_mcangle_other	6.797		10693	29.219
X-RAY DIFFRACTION	r_scbond_it	3.773		14692	17.477
X-RAY DIFFRACTION	r_scbond_other	3.773		14691	17.476
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.535		21158	29.324
X-RAY DIFFRACTION	r_long_range_B_refined	13.563		112217
X-RAY DIFFRACTION	r_long_range_B_other	13.563		112218
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	24886	0.01
1	2	B	24886	0.01
2	1	A	24906	0.01
2	2	C	24906	0.01
3	1	A	24922	0.01
3	2	D	24922	0.01
4	1	A	24870	0.01
4	2	E	24870	0.01
5	1	A	24948	0.01
5	2	F	24948	0.01
6	1	B	24884	0.01
6	2	C	24884	0.01
7	1	B	24898	0.01
7	2	D	24898	0.01
8	1	B	24854	0.01
8	2	E	24854	0.01
9	1	B	24904	0.01
9	2	F	24904	0.01
10	1	C	24896	0.01
10	2	D	24896	0.01
11	1	C	24860	0.01
11	2	E	24860	0.01
12	1	C	24908	0.01
12	2	F	24908	0.01
13	1	D	24862	0.01
13	2	E	24862	0.01
14	1	D	24922	0.01
14	2	F	24922	0.01
15	1	E	24878	0.01
15	2	F	24878	0.01
16	1	G	6154	0.07
16	2	I	6154	0.07
17	1	G	2806	0.05
17	2	K	2806	0.05
18	1	G	2794	0.05
18	2	M	2794	0.05
19	1	H	6346	0.07
19	2	J	6346	0.07
20	1	H	2782	0.03
20	2	L	2782	0.03
21	1	H	2794	0.03
21	2	N	2794	0.03
22	1	I	2814	0.04
22	2	K	2814	0.04
23	1	I	2802	0.04
23	2	M	2802	0.04
24	1	J	2778	0.03
24	2	L	2778	0.03
25	1	J	2794	0.03
25	2	N	2794	0.03
26	1	K	3038	0.01
26	2	M	3038	0.01
27	1	L	2946	0.02
27	2	N	2946	0.02

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	3.3446	-1.4749	-0.0364	4.0604	1.1296	1.627	0.3269	-0.4505	0.7326	-0.3819	0.0001	-0.366	-0.6562	-0.1382	-0.327	0.3995	0.0035	0.1979	0.3429	-0.0512	0.2392	50.36	54.529	75.137
2	2.6882	-1.3209	-0.5591	3.5826	0.9473	2.1542	-0.0072	0.113	-0.1657	-0.445	-0.1326	-0.0539	0.3777	0.343	0.1397	0.2232	0.0971	0.0238	0.2932	0.1024	0.079	-7.399	44.411	41.55
3	2.8907	-0.3408	-0.95	2.5886	0.4117	3.6975	-0.1537	0.1879	-0.1246	-0.4531	0.1344	0.4757	-0.1735	-0.2066	0.0193	0.2292	-0.1801	-0.1516	0.2525	0.0625	0.2002	-52.98	42.026	15.922
4	7.6713	-1.2628	2.5451	0.3514	-0.4363	1.0061	0.3283	0.7348	0.9629	-0.3017	-0.3557	-0.2167	0.1167	0.2902	0.0274	0.7995	0.074	0.1661	0.7871	0.1704	0.6888	30.647	58.647	45.423
5	13.1249	5.1838	8.8744	3.1123	3.7359	7.384	0.9379	-0.6764	0.6588	0.8851	-0.7416	0.6456	1.3466	-0.0982	-0.1963	1.1642	0.0702	0.1266	1.0166	-0.0472	0.9589	14.404	40.387	72.255
6	12.464	0.5587	1.2769	0.6104	0.8083	2.3696	0.2197	0.4322	1.4004	-0.6127	-0.1157	0.3418	-0.7719	-0.3822	-0.104	1.1136	-0.1247	-0.1718	0.7196	0.2105	0.6614	-56.06	60.138	7.586
7	2.9202	0.7786	2.2183	0.867	1.7926	10.7326	0.4848	0.1427	-0.287	-0.1939	-0.3846	0.3352	1.8112	-0.5059	-0.1002	1.1861	0.0269	-0.3381	0.8123	0.0691	0.8708	-60.373	23.034	18.674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	149 - 601
2	X-RAY DIFFRACTION	1	B	149 - 601
3	X-RAY DIFFRACTION	2	C	149 - 601
4	X-RAY DIFFRACTION	2	D	149 - 601
5	X-RAY DIFFRACTION	3	E	149 - 601
6	X-RAY DIFFRACTION	3	F	149 - 601
7	X-RAY DIFFRACTION	4	G	2 - 38
8	X-RAY DIFFRACTION	4	H	3 - 38
9	X-RAY DIFFRACTION	5	I	2 - 37
10	X-RAY DIFFRACTION	5	J	3 - 38
11	X-RAY DIFFRACTION	6	K	20 - 36
12	X-RAY DIFFRACTION	6	L	4 - 20
13	X-RAY DIFFRACTION	7	M	20 - 36
14	X-RAY DIFFRACTION	7	N	4 - 20

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