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- PDB-4k96: Structure of Binary Complex of cGAS with Bound dsDNA -

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Basic information

Entry
Database: PDB / ID: 4k96
TitleStructure of Binary Complex of cGAS with Bound dsDNA
Components
  • Cyclic GMP-AMP synthase
  • DNA-F
  • DNA-R
KeywordsTRANSFERASE/DNA / nucleotidyltransferase fold / 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 / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor 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 / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / regulation of immune response / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / 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 / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / SAD / Resolution: 2.084 Å
AuthorsGao, P. / Wu, Y. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.
Authors: Gao, P. / Ascano, M. / Wu, Y. / Barchet, W. / Gaffney, B.L. / Zillinger, T. / Serganov, A.A. / Liu, Y. / Jones, R.A. / Hartmann, G. / Tuschl, T. / Patel, D.J.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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
B: Cyclic GMP-AMP synthase
E: DNA-F
F: DNA-R
G: DNA-F
H: DNA-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9818
Polymers105,8506
Non-polymers1312
Water13,007722
1
A: Cyclic GMP-AMP synthase
E: DNA-F
F: DNA-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9904
Polymers52,9253
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area22800 Å2
MethodPISA
2
B: Cyclic GMP-AMP synthase
G: DNA-F
H: DNA-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9904
Polymers52,9253
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-54 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.910, 93.801, 75.509
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42512.121 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, 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, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: DNA chain DNA-F


Mass: 5253.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol
#3: DNA chain DNA-R


Mass: 5159.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol
#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 / Water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M MES, 8% MPD, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.084→50 Å / Num. all: 74501 / Num. obs: 74352 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.084→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.084→45.066 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 2000 2.69 %RANDOM
Rwork0.2016 ---
obs0.2023 74352 98.96 %-
all-74501 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.084→45.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 1382 2 722 7981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037528
X-RAY DIFFRACTIONf_angle_d0.94710408
X-RAY DIFFRACTIONf_dihedral_angle_d19.9812984
X-RAY DIFFRACTIONf_chiral_restr0.0771130
X-RAY DIFFRACTIONf_plane_restr0.0031084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0838-2.13590.27851260.25164559X-RAY DIFFRACTION88
2.1359-2.19370.29561430.24055187X-RAY DIFFRACTION100
2.1937-2.25820.27871450.22825206X-RAY DIFFRACTION100
2.2582-2.33110.24181420.2225192X-RAY DIFFRACTION100
2.3311-2.41440.27321440.21965187X-RAY DIFFRACTION100
2.4144-2.51110.27141450.21445219X-RAY DIFFRACTION100
2.5111-2.62530.26241440.21235225X-RAY DIFFRACTION100
2.6253-2.76370.25681430.22795182X-RAY DIFFRACTION100
2.7637-2.93690.28991450.21665244X-RAY DIFFRACTION100
2.9369-3.16360.19671440.21525199X-RAY DIFFRACTION100
3.1636-3.48180.21051440.19845204X-RAY DIFFRACTION100
3.4818-3.98540.21541450.18215255X-RAY DIFFRACTION100
3.9854-5.02010.18961450.16765245X-RAY DIFFRACTION100
5.0201-45.07640.21141450.2065248X-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)
13.9469-1.01620.65091.87770.82442.85630.0993-0.51990.5187-0.0055-0.0343-0.1273-0.4487-0.1194-0.04090.41110.00170.08830.18640.11040.209858.692362.115318.7779
21.3269-0.67520.422.66280.82143.99530.22740.1627-0.0444-0.4377-0.12320.2812-0.2687-0.5819-0.11660.34630.07770.03040.36510.10880.283148.68454.47093.5014
31.5472-0.7421.3731.2287-0.86173.5620.03410.24340.0692-0.4211-0.0159-0.02340.0238-0.0959-0.08290.24750.0219-0.00690.21320.00510.189458.943741.48863.6379
42.27280.6542-0.31463.10480.49042.52750.06650.38840.2498-0.61810.1597-0.4159-0.33970.6332-0.08430.2989-0.07790.14430.40140.02190.352376.546451.79576.2609
57.3519-0.98090.66971.86971.45782.64520.40911.1008-0.6-0.1378-0.1653-0.0790.3413-0.1434-0.18620.2757-0.0521-0.02840.13370.06680.233956.26318.653122.8909
62.7566-0.4889-0.77283.11040.41022.2890.14910.2789-0.0413-0.1224-0.14270.2951-0.0144-0.5143-0.03520.187-0.0408-0.05610.25940.00970.160548.052217.124227.9222
74.85471.3174-1.02865.3218-0.53443.6536-0.2545-0.48940.68030.57210.10970.949-0.7524-0.73130.00850.44260.12970.17140.42890.01540.419838.391329.972643.778
81.75930.1519-0.81464.05481.92353.23770.0669-0.0335-0.22310.233-0.09340.11980.515-0.50480.01580.2372-0.0766-0.03910.29060.0360.208542.6178.765133.1
92.6991.2258-1.50331.4409-0.10152.05250.0496-0.0138-0.06830.2257-0.05860.090.0584-0.0979-0.01660.22240.0399-0.01610.15150.01520.168853.631729.618337.5071
102.1255-0.64640.40091.379-0.36751.5130.1012-0.0558-0.16440.1325-0.0641-0.13220.0910.1559-0.0110.19450.0159-0.07460.1876-0.01030.245370.802220.026636.5992
114.3148-2.2296-0.41564.4429-0.49981.651-0.3317-0.9098-0.51840.70560.31820.05460.00520.1478-0.02040.3173-0.0292-0.11850.32550.09980.327970.210613.568949.0484
128.7459-0.25482.45969.3739-1.242.0070.03531.112-1.1161-0.76570.40370.9091-0.3872-1.1097-0.31490.44210.06820.00230.7303-0.0240.460138.845149.502524.817
133.4182-1.1074-0.96694.4551-0.36384.2058-0.3926-0.62930.21280.22490.1483-0.4937-0.48650.17540.23430.31340.0586-0.0830.2947-0.04130.247863.249454.131531.6175
145.8913-0.88262.43421.7292-0.15541.4149-0.3839-0.70210.02920.3287-0.0254-0.1812-0.1065-0.0865-0.32080.5175-0.0793-0.5222.31340.20391.274979.532559.755342.7503
155.37145.1706-4.47625.0411-4.04014.9565-0.72640.2264-1.0625-0.5322-0.3913-2.4454-0.29491.39940.37750.05620.1627-0.4031.9276-0.33412.601680.525456.790733.8571
162.2981.0774-2.265.55840.29954.131-0.5199-0.2339-0.3501-0.0330.45860.52680.2251-0.0771-0.19850.37220.02380.08360.29040.12570.420353.597850.194729.431
173.39071.29224.37339.6217-3.31238.4747-1.5326-0.75630.90390.79321.10030.38830.1362-1.38780.31670.56020.1841-0.02331.0818-0.18690.639539.771222.269711.5923
185.36592.42320.88034.35830.44914.1642-0.83030.3428-0.1912-0.59010.33750.2524-0.1229-0.4290.270.25940.01130.0170.3266-0.09040.242358.779423.148710.2056
193.51591.6868-0.79113.645-0.43246.36750.01481.8497-0.3624-0.5534-0.0504-2.00811.01990.6653-0.24670.39690.15480.18420.6401-0.06230.616670.28429.671412.7252
202.07171.04030.52013.76391.97977.1924-0.10622.07590.217-0.91560.0211-2.30940.33442.11440.09490.94290.42490.3462.1344-0.18721.893881.92188.64724.3444
218.6328-6.8801-2.04248.8622-0.51571.8707-0.918-1.32750.46541.12780.7965-0.5372-0.4118-0.2791-0.47280.55320.565-0.02621.6615-0.53631.999482.145110.66512.9274
223.5981-0.43672.57454.2269-1.20981.8678-0.41711.01640.4771-0.29330.0675-0.1224-0.43170.18070.19830.3861-0.021-0.04530.45980.04780.327255.180820.931511.0353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 149 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 376 )
4X-RAY DIFFRACTION4chain 'A' and (resid 377 through 505 )
5X-RAY DIFFRACTION5chain 'B' and (resid 149 through 183 )
6X-RAY DIFFRACTION6chain 'B' and (resid 184 through 219 )
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 258 )
8X-RAY DIFFRACTION8chain 'B' and (resid 259 through 313 )
9X-RAY DIFFRACTION9chain 'B' and (resid 314 through 376 )
10X-RAY DIFFRACTION10chain 'B' and (resid 377 through 470 )
11X-RAY DIFFRACTION11chain 'B' and (resid 471 through 505 )
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 5 )
13X-RAY DIFFRACTION13chain 'E' and (resid 6 through 15 )
14X-RAY DIFFRACTION14chain 'E' and (resid 16 through 17 )
15X-RAY DIFFRACTION15chain 'F' and (resid 1 through 5 )
16X-RAY DIFFRACTION16chain 'F' and (resid 6 through 17 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 5 )
18X-RAY DIFFRACTION18chain 'G' and (resid 6 through 10 )
19X-RAY DIFFRACTION19chain 'G' and (resid 11 through 15 )
20X-RAY DIFFRACTION20chain 'G' and (resid 16 through 17 )
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 5 )
22X-RAY DIFFRACTION22chain 'H' and (resid 6 through 17 )

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