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- PDB-6o47: human cGAS core domain (K427E/K428E) bound with RU-521 -

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Basic information

Entry
Database: PDB / ID: 6o47
Titlehuman cGAS core domain (K427E/K428E) bound with RU-521
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / human / cGAS / core domain / compound / RU-521 / DNA BINDING PROTEIN
Function / homology
Function and homology information


cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / 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 / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / 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
Chem-AEV / CITRIC ACID / Chem-LLS / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsXie, W. / Lama, L. / Adura, C. / Glickman, J.F. / Tuschl, T. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation.
Authors: Xie, W. / Lama, L. / Adura, C. / Tomita, D. / Glickman, J.F. / Tuschl, T. / Patel, D.J.
History
DepositionFeb 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7666
Polymers43,4861
Non-polymers1,2805
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.157, 116.157, 59.951
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cyclic GMP-AMP synthase / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 43486.047 Da / Num. of mol.: 1 / Mutation: K427E, K428E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N884, cyclic GMP-AMP synthase

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Non-polymers , 5 types, 185 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-LLS / (3~{S})-3-[1-[4,5-bis(chloranyl)-1~{H}-benzimidazol-2-yl]-3-methyl-5-oxidanyl-pyrazol-4-yl]-3~{H}-2-benzofuran-1-one


Mass: 415.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H12Cl2N4O3
#5: Chemical ChemComp-AEV / 2-(4,5-dichloro-1H-benzimidazol-2-yl)-5-methyl-4-[(1R)-3-oxo-1,3-dihydro-2-benzofuran-1-yl]-1,2-dihydro-3H-pyrazol-3-one


Mass: 415.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H12Cl2N4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.064 M sodium citrate 7.0, 0.1 M HEPES, pH 7.0, 10% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 23702 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 27.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.025 / Rrim(I) all: 0.083 / Χ2: 0.926 / Net I/σ(I): 33.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 4 / Num. unique obs: 2322 / CC1/2: 0.864 / Rpim(I) all: 0.239 / Rrim(I) all: 0.648 / Χ2: 0.849 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O68

4o68


Resolution: 2.196→29.265 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.96
RfactorNum. reflection% reflection
Rfree0.2214 3457 8.48 %
Rwork0.1815 --
obs0.1848 23668 88.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.196→29.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 83 180 3117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052996
X-RAY DIFFRACTIONf_angle_d0.7514028
X-RAY DIFFRACTIONf_dihedral_angle_d15.3671812
X-RAY DIFFRACTIONf_chiral_restr0.044426
X-RAY DIFFRACTIONf_plane_restr0.004505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.196-2.22610.2425770.2493835X-RAY DIFFRACTION49
2.2261-2.25780.2513850.2449866X-RAY DIFFRACTION52
2.2578-2.29150.2648870.2245946X-RAY DIFFRACTION55
2.2915-2.32730.2511890.2131024X-RAY DIFFRACTION60
2.3273-2.36550.291050.2111106X-RAY DIFFRACTION66
2.3655-2.40620.24421130.22351200X-RAY DIFFRACTION70
2.4062-2.450.26181190.20981314X-RAY DIFFRACTION80
2.45-2.49710.25551410.21211490X-RAY DIFFRACTION88
2.4971-2.5480.25571560.19261607X-RAY DIFFRACTION95
2.548-2.60340.23821470.2081644X-RAY DIFFRACTION97
2.6034-2.66390.2721490.19251670X-RAY DIFFRACTION99
2.6639-2.73050.23061540.19481700X-RAY DIFFRACTION99
2.7305-2.80420.23331520.18621646X-RAY DIFFRACTION100
2.8042-2.88670.19291500.19811707X-RAY DIFFRACTION99
2.8867-2.97980.28341600.19441729X-RAY DIFFRACTION100
2.9798-3.08620.241500.18391645X-RAY DIFFRACTION100
3.0862-3.20960.22031620.18241707X-RAY DIFFRACTION100
3.2096-3.35550.22071620.17731673X-RAY DIFFRACTION100
3.3555-3.53210.20181540.17451697X-RAY DIFFRACTION100
3.5321-3.7530.1891540.16081690X-RAY DIFFRACTION100
3.753-4.0420.18831610.15531658X-RAY DIFFRACTION100
4.042-4.44750.18151550.15551686X-RAY DIFFRACTION100
4.4475-5.08820.17961570.14991693X-RAY DIFFRACTION100
5.0882-6.39950.24471620.19421682X-RAY DIFFRACTION100
6.3995-29.26770.24391560.18761695X-RAY DIFFRACTION100

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