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- PDB-4lez: Structure of mouse cGAS bound to an 18bp DNA and cGAS product -

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Basic information

Entry
Database: PDB / ID: 4lez
TitleStructure of mouse cGAS bound to an 18bp DNA and cGAS product
Components
  • 18bp dsDNA
  • Cyclic GMP-AMP synthase
KeywordsTRANSFERASE/DNA / NTase / DNA sensor / TRANSFERASE-DNA complex
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 ...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 / cGMP-mediated signaling / cellular response to exogenous dsRNA / regulation of immune response / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / cAMP-mediated signaling / molecular condensate scaffold activity / determination of adult lifespan / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cGAMP / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLi, P.
CitationJournal: 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
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Aug 5, 2015Group: Non-polymer description
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
C: Cyclic GMP-AMP synthase
E: 18bp dsDNA
F: 18bp dsDNA
I: 18bp dsDNA
J: 18bp dsDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,50710
Polymers108,0286
Non-polymers1,4804
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.209, 99.031, 142.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / m-cGAS / Mab-21 domain-containing protein 1


Mass: 42984.664 Da / Num. of mol.: 2 / Fragment: mouse cGAS catalytic domain, UNP residues 142-507
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: DNA chain
18bp dsDNA


Mass: 5514.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic 18 bp dsDNA
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Details: Cyclic GAMP synthesized using cGAS
#4: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24-36% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2013 / Details: osmic
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.36→33.5 Å / Num. all: 47070 / Num. obs: 45447 / % possible obs: 96.6 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 6.2 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069
Reflection shellResolution: 2.36→2.43 Å / % possible all: 97

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→33.549 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1999 4.4 %Random
Rwork0.1922 ---
obs0.1946 45447 96.61 %-
all-47070 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→33.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 1464 92 151 7645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087808
X-RAY DIFFRACTIONf_angle_d1.22910826
X-RAY DIFFRACTIONf_dihedral_angle_d20.9173098
X-RAY DIFFRACTIONf_chiral_restr0.0741174
X-RAY DIFFRACTIONf_plane_restr0.0071108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3564-2.41530.3571380.30442991X-RAY DIFFRACTION94
2.4153-2.48050.3311400.27653048X-RAY DIFFRACTION96
2.4805-2.55350.34681400.2593044X-RAY DIFFRACTION96
2.5535-2.63590.36851390.25453038X-RAY DIFFRACTION96
2.6359-2.73010.31191390.2493026X-RAY DIFFRACTION96
2.7301-2.83930.3281410.24643048X-RAY DIFFRACTION96
2.8393-2.96850.30171400.23913054X-RAY DIFFRACTION96
2.9685-3.12490.3041390.2393035X-RAY DIFFRACTION95
3.1249-3.32050.25451400.2123034X-RAY DIFFRACTION95
3.3205-3.57660.32471420.19153071X-RAY DIFFRACTION96
3.5766-3.9360.24991450.1853169X-RAY DIFFRACTION98
3.936-4.50440.21391490.1573229X-RAY DIFFRACTION99
4.5044-5.67060.18161510.15993282X-RAY DIFFRACTION100
5.6706-33.55260.19171560.16383409X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.4833-0.59390.61193.8606-0.05692.6345-0.1682-0.4271-0.26250.69020.0799-0.098-0.0171-0.09130.10320.4240.07940.03460.37410.06830.3998-9.9545-28.888927.5411
26.48684.5438-0.87124.3303-0.69815.32130.6613-1.71291.25962.0594-0.3617-0.22730.23790.8841-0.39021.13640.0737-0.27370.9938-0.16290.99644.7778-17.861845.0163
31.4444-1.55080.85024.5703-1.43461.8018-0.225-0.1580.05650.67120.0702-0.50470.06030.1410.15050.50420.0379-0.06880.44920.0560.4361-3.9425-26.087528.2904
42.4498-2.0774-0.60634.7841.00131.76740.20030.47840.1517-0.2666-0.1937-0.53310.14350.2875-0.02440.40870.05840.05530.47330.06320.4442-3.6506-27.95756.0489
53.5333-1.24080.24834.09771.22462.1455-0.4324-0.69950.23390.96730.2951-0.0257-0.03310.04970.13480.59380.1791-0.11950.4641-0.03930.3899-29.23419.615126.817
62.187-1.49280.25075.03441.29960.9896-0.5451-0.693-0.03641.22610.28970.68780.0832-0.28740.20990.64170.14310.10380.60530.00630.3998-36.31465.666330.162
73.0302-1.86840.15855.5096-1.16782.3660.07410.38440.0144-0.224-0.1050.6303-0.4726-0.30920.02920.4590.0476-0.09940.4735-0.01690.4067-35.9837.5675.5002
85.5685-0.7526-1.37356.88761.03437.4162-1.3755-0.20331.4744-0.07010.5236-0.2798-0.9505-1.0230.84371.9312-0.2831-0.09631.6965-0.33270.8392-29.0934-15.05752.6082
92.855-0.1247-1.54612.9320.19956.72080.4013-0.5286-0.23180.518-0.03520.08231.0497-0.2896-0.33630.5207-0.1436-0.10040.51430.05720.5793-29.7327-26.794424.2742
105.36751.04891.94565.7511.41754.26590.2888-0.21630.4361-0.4442-0.27450.8151-0.4504-0.8027-0.08990.57360.0310.01040.56310.07810.5834-30.0558-27.671220.177
115.75560.3987-5.93318.1263-2.43996.76241.3102-1.01020.76111.02010.445-0.2923-0.9914-0.321-1.65391.1968-0.3026-0.01061.1133-0.05450.6136-33.0309-19.243442.4503
129.5695-1.1955-0.23683.38613.14032.97621.7664-2.1897-1.14810.50530.2603-1.6765-0.02460.4518-1.69851.4743-0.5836-0.24922.2109-0.04891.0299-26.3066-21.754256.1004
133.8846-1.0058-3.84432.16791.26424.01240.3364-0.90281.12931.09510.35920.40191.2921-1.5906-0.7621.06250.0515-0.09771.2357-0.1030.7122-11.97044.357939.6434
144.66190.8631.63298.27933.12893.5330.20930.04060.5997-0.11770.4669-0.2875-0.54891.5501-0.68680.5076-0.0927-0.02940.5721-0.06530.5153-8.41832.508821.5741
157.49163.7264-0.07378.90552.61282.59270.48490.80821.2248-0.6063-0.5622-1.1087-0.82141.54110.16390.8363-0.2712-0.06340.90210.33650.9885-9.540815.88188.8645
167.35473.79433.90024.82573.43562.76151.1972-0.52750.14890.13430.46080.0944-0.70440.5061-1.25271.0334-0.32440.35321.83370.40641.5311-0.485214.1412-3.4087
170.28710.5560.55182.85130.48141.28910.96170.2823-0.62870.4330.22520.04410.2959-1.72110.05621.7684-0.79750.52783.07340.51710.5806-7.728411.3038-1.696
185.75451.4773-5.8745.056-1.00366.0131-0.2559-0.62880.965-0.42530.4105-0.38350.46122.4555-0.25080.6077-0.0769-0.22190.89740.00480.7201-5.707313.048215.8214
193.0433-1.77732.76853.6485-3.05215.38870.1332-0.4187-0.46010.43520.03380.0053-0.2279-0.0164-0.1930.55970.0136-0.18740.4970.0010.664-14.26711.34528.1971
207.797-3.7827-2.48283.27920.04052.8820.5749-2.30090.86841.30251.8929-1.5148-1.25710.9244-0.25762.29530.1301-0.65791.3926-0.19690.7156-6.4772-1.539341.9762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 376 )
4X-RAY DIFFRACTION4chain 'A' and (resid 377 through 507 )
5X-RAY DIFFRACTION5chain 'C' and (resid 149 through 239 )
6X-RAY DIFFRACTION6chain 'C' and (resid 240 through 376 )
7X-RAY DIFFRACTION7chain 'C' and (resid 377 through 507 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 5 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 18 )
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 10 )
11X-RAY DIFFRACTION11chain 'F' and (resid 11 through 15 )
12X-RAY DIFFRACTION12chain 'F' and (resid 16 through 18 )
13X-RAY DIFFRACTION13chain 'I' and (resid 1 through 5 )
14X-RAY DIFFRACTION14chain 'I' and (resid 6 through 10 )
15X-RAY DIFFRACTION15chain 'I' and (resid 11 through 15 )
16X-RAY DIFFRACTION16chain 'I' and (resid 16 through 18 )
17X-RAY DIFFRACTION17chain 'J' and (resid 1 through 5 )
18X-RAY DIFFRACTION18chain 'J' and (resid 6 through 10 )
19X-RAY DIFFRACTION19chain 'J' and (resid 11 through 15 )
20X-RAY DIFFRACTION20chain 'J' and (resid 16 through 18 )

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