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- PDB-4k97: Structure of Ternary Complex of cGAS with dsDNA and Bound ATP -

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Basic information

Entry
Database: PDB / ID: 4k97
TitleStructure of Ternary Complex of cGAS with dsDNA and Bound ATP
Components
  • Cyclic GMP-AMP synthase
  • DNA-F
  • DNA-R
KeywordsTRANSFERASE/DNA / nucleotidyltransferase fold / TRANSFERASE-DNA complex
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of type I interferon production / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / negative regulation of DNA repair / cGMP-mediated signaling / cellular response to exogenous dsRNA / positive regulation of type I interferon production / nucleosome binding / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / positive regulation of defense response to virus by host / activation of innate immune response / phosphatidylinositol-4,5-bisphosphate binding / cAMP-mediated signaling / determination of adult lifespan / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / innate immune response / DNA repair / 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 / Mab-21-like, nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Mab-21 protein nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Beta Polymerase; domain 2 ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Mab-21-like, nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Mab-21 protein nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
D: DNA-F
E: DNA-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5467
Polymers52,9253
Non-polymers6214
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-39 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.204, 99.373, 131.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42512.121 Da / Num. of mol.: 1 / 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

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain DNA-F


Mass: 5253.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol
#3: DNA chain DNA-R


Mass: 5159.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by regular protocol

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Non-polymers , 4 types, 127 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M HEPES, 0.2 M CaAc2, 20% PEG300, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9823 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9823 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. all: 22187 / Num. obs: 22099 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.41→2.54 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→49.69 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2000 9.05 %
Rwork0.193 --
obs0.197 22099 99.6 %
all-22187 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 592 34 123 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073691
X-RAY DIFFRACTIONf_angle_d1.195097
X-RAY DIFFRACTIONf_dihedral_angle_d22.1271458
X-RAY DIFFRACTIONf_chiral_restr0.071551
X-RAY DIFFRACTIONf_plane_restr0.004532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.47030.27971380.25071388X-RAY DIFFRACTION99
2.4703-2.53710.3431430.24461427X-RAY DIFFRACTION100
2.5371-2.61170.27931390.24351409X-RAY DIFFRACTION100
2.6117-2.6960.31151420.23221424X-RAY DIFFRACTION100
2.696-2.79240.29071420.23891424X-RAY DIFFRACTION100
2.7924-2.90420.30961420.23771427X-RAY DIFFRACTION100
2.9042-3.03630.2631400.23621402X-RAY DIFFRACTION100
3.0363-3.19640.29081440.23351457X-RAY DIFFRACTION100
3.1964-3.39660.29321410.21051413X-RAY DIFFRACTION100
3.3966-3.65880.23641430.1881437X-RAY DIFFRACTION99
3.6588-4.02680.20781430.17521443X-RAY DIFFRACTION100
4.0268-4.60910.17781450.15141455X-RAY DIFFRACTION100
4.6091-5.80560.20611450.15141457X-RAY DIFFRACTION99
5.8056-49.6970.20061530.18471536X-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)
13.0836-0.4411-0.06863.96720.09262.18540.07420.04850.7112-0.1109-0.06740.249-0.9228-0.79210.2330.2238-0.04690.02080.27110.0630.444312.7922222.8185171.9899
23.0188-1.0103-0.42954.46361.36434.06190.15230.5118-0.0118-0.5712-0.1172-0.0726-0.33750.0204-0.11020.4553-0.01180.10260.40110.03980.401814.7191213.7096164.4162
31.32950.2887-0.14812.7832-0.93431.34170.03460.3329-0.0537-0.4354-0.1339-0.4134-0.03980.29910.06270.3189-0.00210.07470.3825-0.00550.299721.774204.8325163.8337
43.57790.35290.44233.09691.41491.63490.0165-0.50630.16740.10230.133-0.3973-0.05330.5017-0.16220.3041-0.0370.01360.41710.02390.238422.5301207.6434187.8906
55.3673-0.4376-1.33074.90411.23632.75870.3490.89610.5534-0.56550.1246-0.0994-1.0521-0.6244-0.41270.59360.02830.12020.5080.08320.4255-1.4378218.7983170.6468
65.36520.38010.65975.3611.7172.69730.13910.06550.05040.17310.21650.31720.561-1.3854-0.28790.5132-0.07380.04540.68330.190.4093-3.2218217.1977172.0843
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 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 376 )
4X-RAY DIFFRACTION4chain 'A' and (resid 377 through 505 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 15 )
6X-RAY DIFFRACTION6chain 'E' and (resid 4 through 17 )

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