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- PDB-4kb6: Structure of porcine cyclic GMP AMP synthase (CGAS) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4kb6
TitleStructure of porcine cyclic GMP AMP synthase (CGAS) in complex with DNA, ATP and GTP
Components
  • DNA (5'-D(P*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
  • Uncharacterized protein
KeywordsTRANSFERASE/DNA / OAS-like fold / Receptor / Immunity / cGAS / double stranded DNA / GTP / cytosol / TRANSFERASE-DNA complex
Function / homology
Function and homology information


cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cGMP-mediated signaling / cAMP-mediated signaling ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / cGAS/STING signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / molecular condensate scaffold activity / 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 / metal ion binding / nucleus / 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
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesSus scrofa (pig)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0754 Å
AuthorsDeimling, T. / Hopfner, K.-P.
CitationJournal: Nature / Year: 2013
Title: Structural mechanism of cytosolic DNA sensing by cGAS.
Authors: Civril, F. / Deimling, T. / de Oliveira Mann, C.C. / Ablasser, A. / Moldt, M. / Witte, G. / Hornung, V. / Hopfner, K.P.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references / Structure summary
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: DNA (5'-D(P*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
C: DNA (5'-D(P*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1547
Polymers51,0343
Non-polymers1,1204
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.280, 111.890, 117.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#1: Protein Uncharacterized protein


Mass: 42470.191 Da / Num. of mol.: 1 / Fragment: UNP Residues 135-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: I3LM39
#2: DNA chain DNA (5'-D(P*CP*GP*AP*CP*GP*CP*TP*AP*GP*CP*GP*TP*CP*G)-3')


Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 14mer ds DNA / Source: (synth.) Synthetic DNA (others)

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Non-polymers , 5 types, 6 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 137 AND 138 ARE POLYMORPHIC CHANGES IN THE SEQUENCE

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Na-cacodylate, 2.5 mM spermine, 60 mM magnesium chloride, 3 % PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.07→999 Å / Num. all: 10913 / Num. obs: 10762 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.07-3.25191.7
3.26-3.471100
3.48-3.751100
3.76-4.111100
4.12-4.6199.8
4.61-5.31100
5.31-6.49199.9
6.5-9.14199.7
9.15-999198.9

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Processing

Software
NameVersionClassification
MxCuBEHamburgdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JLX

4jlx


Resolution: 3.0754→68.325 Å / SU ML: 0.3 / σ(F): 2.03 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 538 5.01 %Random
Rwork0.2545 ---
obs0.2547 10739 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0754→68.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 555 65 2 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043652
X-RAY DIFFRACTIONf_angle_d0.8885042
X-RAY DIFFRACTIONf_dihedral_angle_d24.4541399
X-RAY DIFFRACTIONf_chiral_restr0.058544
X-RAY DIFFRACTIONf_plane_restr0.003530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0754-3.38490.33381260.31432396X-RAY DIFFRACTION95
3.3849-3.87470.30461340.28532544X-RAY DIFFRACTION100
3.8747-4.88150.25021360.25282578X-RAY DIFFRACTION100
4.8815-68.34220.23271420.23452683X-RAY DIFFRACTION100

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