PDB-8g2p: Structure of Ternary Complex of cGAS with dsDNA and Bound ATP and GTP

ID or keywords:

Entry

Database: PDB / ID: 8g2p

Title

Structure of Ternary Complex of cGAS with dsDNA and Bound ATP and GTP

Components

Cyclic GMP-AMP synthase
Palindromic DNA18

Keywords

TRANSFERASE/DNA / Transferase-DNA complex / cGAS / substrates-bound / IMMUNE SYSTEM

Function / homology

Function and homology information

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

Biological species

Mus musculus (house mouse)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.521 Å

Authors

Wu, S. / Sohn, J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structure of Ternary Complex of cGAS with dsDNA and Bound ATP and GTP
Authors: Wu, S. / Sohn, J.

History

Deposition	Feb 6, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8g2p.cif.gz	914.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8g2p.ent.gz	583.3 KB	Display	PDB format
PDBx/mmJSON format	8g2p.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/g2/8g2p ftp://data.pdbj.org/pub/pdb/validation_reports/g2/8g2p	HTTPS FTP

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Related structure data

Similar structure data	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

C: Cyclic GMP-AMP synthase

E: Palindromic DNA18

F: Palindromic DNA18

I: Palindromic DNA18

J: Palindromic DNA18

hetero molecules

110 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	78.219, 99.102, 141.944
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A
13	7	A
14	7	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	149 - 507
2	1	1	A	149 - 507
3	2	2	A	1 - 18
4	2	2	A	1 - 18
5	3	3	A	1 - 18
6	3	3	A	1 - 18
7	4	4	A	1 - 18
8	4	4	A	1 - 18
9	5	5	A	1 - 18
10	5	5	A	1 - 18
11	6	6	A	1 - 18
12	6	6	A	1 - 18
13	7	7	A	1 - 18
14	7	7	A	1 - 18

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14

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Protein / DNA chain , 2 types, 6 molecules ACEFIJ

#1: Protein	Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / m-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1 Mass: 42639.266 Da / Num. of mol.: 2 / Mutation: D307N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT WT Details (production host): His6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance Production host: Escherichia coli BL21(DE3)* (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: DNA chain	Palindromic DNA18 Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#1: Protein

Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / m-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1

Mass: 42639.266 Da / Num. of mol.: 2 / Mutation: D307N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Plasmid: nHMT mCAT WT
Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance
Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase

#2: DNA chain

Palindromic DNA18

Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 123 molecules

#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 52 % / Description: polarizes nicely
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium acetate, 32% MPD, with 0.1 M Bis-Tris pH 6.5 PH range: 6.0-7.0 / Temp details: 4-degree Celsius in cold room

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 17-ID-2 / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2022

Radiation

Monochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.52→29.78 Å / Num. obs: 37823 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.044 / R_rim(I) all: 0.083 / Net I/σ(I): 14.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9.09-29.76	6	0.027	871	0.999	0.017	0.032
2.52-2.62	6.7	0.696	4211	0.785	0.429	0.82

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Processing

Software

Name	Version	Classification
XDS	20210205	data reduction
Aimless	0.7.7	data scaling
MOLREP	11.7.03	phasing
Coot	0.9.6	model building
REFMAC	5.8.0403	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.521→29.773 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.932 / SU B: 19.492 / SU ML: 0.219 / Cross valid method: FREE R-VALUE / ESU R: 0.54 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2419	1898	5.026 %
R_work	0.1899	35867	-
all	0.192	-	-
obs	-	37765	99.473 %

Solvent computation

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

Displacement parameters

B_iso mean: 66.529 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.157 Å²	0 Å²	0 Å²
2-	-	0.639 Å²	-0 Å²
3-	-	-	-0.796 Å²

Refinement step

Cycle: LAST / Resolution: 2.521→29.773 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5738	1464	130	115	7447

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	7716
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	6593
X-RAY DIFFRACTION	r_angle_refined_deg	1.868	1.694	10624
X-RAY DIFFRACTION	r_angle_other_deg	0.491	1.573	15329
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.851	5	685
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.346	5	36
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.375	5	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.865	10	1169
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.179	10	275
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1162
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7484
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1582
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	1416
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	5893
X-RAY DIFFRACTION	r_nbtor_refined	0.197	0.2	3493
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3724
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.2	174
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.075	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.43	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.235	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.199	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.211	0.2	6
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_paralell_plane_angle_deg	5.656	1.2	66
X-RAY DIFFRACTION	r_mcbond_it	2.93	3.343	2764
X-RAY DIFFRACTION	r_mcbond_other	2.928	3.344	2764
X-RAY DIFFRACTION	r_mcangle_it	4.582	5.997	3441
X-RAY DIFFRACTION	r_mcangle_other	4.582	5.998	3442
X-RAY DIFFRACTION	r_scbond_it	3.489	3.898	4952
X-RAY DIFFRACTION	r_scbond_other	3.488	3.899	4953
X-RAY DIFFRACTION	r_scangle_it	5.185	6.995	7193
X-RAY DIFFRACTION	r_scangle_other	5.184	6.995	7193
X-RAY DIFFRACTION	r_lrange_it	7.41	62.337	16208
X-RAY DIFFRACTION	r_lrange_other	7.41	62.341	16206
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.125	0.05	10800
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.115	0.05	1493
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.15	0.05	1469
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.121	0.05	1494
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.136	0.05	1499
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.106	0.05	1517
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.124	0.05	1516

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.12493	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.12493	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11465	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11465	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.14988	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.14988	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12108	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12108	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.13622	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.13622	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10639	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10639	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.12368	0.05008
7	14	A	X-RAY DIFFRACTION	Local ncs	0.12368	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.521-2.586	0.327	126	0.258	2483	0.261	2756	0.935	0.955	94.6662	0.244
2.586-2.657	0.294	149	0.25	2512	0.253	2661	0.948	0.961	100	0.237
2.657-2.733	0.309	118	0.235	2493	0.238	2611	0.942	0.968	100	0.216
2.733-2.816	0.268	126	0.222	2407	0.224	2533	0.957	0.972	100	0.201
2.816-2.908	0.278	118	0.222	2345	0.225	2463	0.953	0.971	100	0.199
2.908-3.009	0.296	119	0.234	2284	0.238	2403	0.943	0.966	100	0.211
3.009-3.121	0.268	128	0.218	2145	0.221	2275	0.952	0.97	99.9121	0.196
3.121-3.247	0.259	99	0.21	2124	0.212	2223	0.956	0.974	100	0.192
3.247-3.39	0.242	101	0.195	2048	0.197	2150	0.963	0.977	99.9535	0.181
3.39-3.553	0.217	107	0.191	1930	0.193	2037	0.972	0.98	100	0.181
3.553-3.742	0.249	114	0.189	1832	0.193	1947	0.959	0.98	99.9486	0.18
3.742-3.965	0.205	91	0.181	1778	0.182	1869	0.97	0.981	100	0.173
3.965-4.234	0.203	99	0.171	1636	0.173	1735	0.973	0.983	100	0.167
4.234-4.565	0.228	91	0.153	1547	0.157	1638	0.971	0.986	100	0.153
4.565-4.989	0.23	70	0.157	1441	0.161	1511	0.972	0.985	100	0.16
4.989-5.559	0.219	67	0.177	1327	0.179	1396	0.973	0.983	99.8567	0.179
5.559-6.382	0.279	68	0.198	1157	0.203	1225	0.962	0.981	100	0.2
6.382-7.728	0.228	46	0.189	1022	0.19	1068	0.973	0.982	100	0.195
7.728-10.578	0.185	35	0.129	826	0.131	862	0.982	0.991	99.884	0.146
10.578-29.773	0.237	26	0.205	530	0.206	557	0.967	0.973	99.8205	0.23

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	2.6524	0.939	0.2584	3.3945	0.1081	1.8034	-0.0152	0.2143	-0.2757	-0.2952	-0.0125	0.2937	0.2385	-0.2302	0.0277	0.0862	-0.0294	-0.0198	0.0554	-0.0418	0.083	5.349	-27.37	-20.176
2	2.8981	1.1846	-0.0727	3.649	-0.6984	2.013	-0.1302	0.3447	0.341	-0.202	0.0717	-0.3132	-0.3352	0.2605	0.0585	0.1254	-0.0699	-0.0153	0.0785	0.0516	0.1237	33.647	8.134	-19.032
3	5.2463	1.3927	-2.1887	2.7922	2.2676	5.6934	0.0438	1.1623	0.0997	-0.761	0.3285	0.0044	-0.2373	0.0926	-0.3723	0.5937	0.2711	-0.1147	0.4701	-0.0911	0.1107	29.194	-23.393	-31.668
4	3.7502	0.2668	-1.6326	3.7874	-0.7782	7.5703	0.3586	0.832	0.0738	-0.6316	-0.1229	-0.072	-0.4075	0.5848	-0.2357	0.2522	0.0448	0.0641	0.3293	-0.0461	0.1317	29.827	-23.897	-32.254
5	5.6478	1.9756	2.8962	6.3841	-1.5928	2.8357	0.0393	-0.526	0.4343	0.1702	0.0724	0.3642	-0.0964	-0.5632	-0.1116	0.1917	0.1792	0.0102	0.3364	0.1691	0.4052	8.336	8.636	-17.993
6	6.9224	0.5709	0.795	7.8019	1.6506	4.5639	0.0927	-0.8456	0.5277	0.3083	0.2356	0.4908	0.1393	-0.542	-0.3284	0.2834	-0.003	-0.1004	0.2611	0.0955	0.2601	8.784	6.859	-18.597

Refinement TLS group

Selection: ALL

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