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- PDB-4o6a: Mouse cyclic GMP-AMP synthase (cGAS) in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4o6a
TitleMouse cyclic GMP-AMP synthase (cGAS) in complex with DNA
Components
  • Cyclic GMP-AMP synthase
  • DNA1
  • DNA2
KeywordsTRANSFERASE/DNA / immune response / 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
DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å
AuthorsZhang, X. / Chen, Z. / Zhang, X.W. / Chen, Z.J.
CitationJournal: Cell Rep / Year: 2014
Title: The Cytosolic DNA Sensor cGAS Forms an Oligomeric Complex with DNA and Undergoes Switch-like Conformational Changes in the Activation Loop.
Authors: Zhang, X. / Wu, J. / Du, F. / Xu, H. / Sun, L. / Chen, Z. / Brautigam, C.A. / Zhang, X. / Chen, Z.J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
D: DNA1
E: DNA2
B: Cyclic GMP-AMP synthase
C: DNA1
F: DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0698
Polymers105,9386
Non-polymers1312
Water18,8981049
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-42 kcal/mol
Surface area42200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.711, 96.330, 75.989
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-977-

HOH

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Components

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


Mass: 42556.238 Da / Num. of mol.: 2 / Fragment: 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, cyclic GMP-AMP synthase
#2: DNA chain DNA1


Mass: 5253.451 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA2


Mass: 5159.343 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% Methanol, 0.1M Tris-HCl, pH 8.0, 0.01M MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 109546 / Num. obs: 109036 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.86→1.89 Å / % possible all: 93.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.859→36.658 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 2000 1.83 %
Rwork0.1865 --
obs0.1871 109023 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.859→36.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 1283 2 1049 8279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077517
X-RAY DIFFRACTIONf_angle_d1.18910370
X-RAY DIFFRACTIONf_dihedral_angle_d19.1212986
X-RAY DIFFRACTIONf_chiral_restr0.0711122
X-RAY DIFFRACTIONf_plane_restr0.0041098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8591-1.90560.24731280.2146873X-RAY DIFFRACTION90
1.9056-1.95710.26321440.21137674X-RAY DIFFRACTION100
1.9571-2.01470.22261430.20217670X-RAY DIFFRACTION100
2.0147-2.07970.21991440.1967686X-RAY DIFFRACTION100
2.0797-2.15410.24771430.19537688X-RAY DIFFRACTION100
2.1541-2.24030.23811450.19377701X-RAY DIFFRACTION100
2.2403-2.34220.23611430.19787671X-RAY DIFFRACTION100
2.3422-2.46570.24441450.19627730X-RAY DIFFRACTION100
2.4657-2.62020.24041430.20187706X-RAY DIFFRACTION100
2.6202-2.82240.23061440.20437688X-RAY DIFFRACTION100
2.8224-3.10630.24671440.20087715X-RAY DIFFRACTION100
3.1063-3.55540.20811450.18127731X-RAY DIFFRACTION100
3.5554-4.47820.17941440.16417758X-RAY DIFFRACTION100
4.4782-36.66540.20271450.17357732X-RAY DIFFRACTION98
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)
10.14490.193-0.08310.2949-0.04640.2627-0.00180.1954-0.00930.02340.0735-0.15740.1633-0.03120.00210.1921-0.0163-0.04270.1828-0.02020.207-33.5929-28.634623.4152
20.22360.2006-0.17830.3141-0.18980.16980.0740.05470.00030.21060.0252-0.0499-0.0573-0.09660.03790.19290.0182-0.00380.14870.02150.142-44.8248-15.084834.8075
30.004-0.0070.01440.0054-0.00470.0159-0.01230.02570.13590.0412-0.07560.16-0.1082-0.1356-0.03510.29680.08210.14140.3270.06530.309-60.9754-8.501441.0596
40.14520.1616-0.12140.4506-0.13790.57420.06540.0204-0.03950.22670.0157-0.05990.0546-0.09440.03020.1605-0.01170.00420.13070.00580.1248-43.0065-17.537335.4798
50.5979-0.25290.11450.6541-0.09770.628-0.0069-0.062-0.10930.213-0.0242-0.2229-0.14060.07860.16760.14840.0058-0.07860.17110.02150.2287-20.9271-19.095240.1252
60.0550.12810.020.2046-0.1020.1673-0.26580.2834-0.1171-0.1720.0633-0.01050.1449-0.1516-0.02060.21310.00080.03320.2858-0.050.2261-34.7068-18.845311.5324
70.03910.11650.05720.2353-0.0590.0603-0.19440.43770.0302-0.07950.0299-0.080.0050.008900.22060.00780.00340.32380.0330.2616-33.1428-16.865510.9547
80.1968-0.34930.07970.6443-0.45970.59560.0780.11970.0839-0.0659-0.0713-0.014-0.1755-0.07070.00180.2399-0.0080.04730.17970.01220.176-37.418217.139410.3992
90.3605-0.11560.09170.3417-0.11110.42030.1250.07830.0197-0.16660.02040.0036-0.2741-0.24430.29210.32030.05010.02040.22970.0370.1384-46.078120.56952.5744
100.3861-0.15430.12540.80290.01280.51710.05350.12850.0726-0.1712-0.1055-0.2198-0.05450.1795-0.02220.1127-0.02870.05070.19150.05850.1683-22.75099.92128.2464
110.03560.0445-0.03840.0224-0.0027-0.0045-0.03020.6134-0.1112-0.5498-0.18-0.31160.08140.4241-0.19370.1294-0.22470.3530.31560.34650.1784-14.449917.5064-1.3533
120.1593-0.1613-0.14360.1617-0.02670.2141-0.2733-0.1670.06820.26030.17310.0415-0.372-0.0455-0.01340.2610.0046-0.03750.1707-0.00780.2041-36.690615.552829.9283
130.00280.00090.0030.00560.0060.0063-0.0488-0.0012-0.0177-0.0662-0.0125-0.05280.03120.00750.00021.2918-0.136-0.44311.4848-0.04431.1032-13.210823.406943.681
140.1205-0.1338-0.13790.2517-0.02690.1158-0.1183-0.0909-0.20.12060.1112-0.0929-0.2242-0.04490.00010.25830.0261-0.00830.18870.01590.2387-32.18814.242131.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 146 through 184 )
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 258 )
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 376 )
5X-RAY DIFFRACTION5chain 'A' and (resid 377 through 506 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'E' and (resid 4 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 239 )
9X-RAY DIFFRACTION9chain 'B' and (resid 240 through 314 )
10X-RAY DIFFRACTION10chain 'B' and (resid 315 through 461 )
11X-RAY DIFFRACTION11chain 'B' and (resid 462 through 506 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 15 )
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 17 )
14X-RAY DIFFRACTION14chain 'F' and (resid 2 through 17 )

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