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- PDB-8wr8: The Crystal Structure of cGAS from Biortus -

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Basic information

Entry
Database: PDB / ID: 8wr8
TitleThe Crystal Structure of cGAS from Biortus
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / DNA-binding / Nucleotidyltransferase / Antiviral defense / DNA damage / DNA repair / Host-virus interaction / Immunity / Innate immunity / ATP-binding / GTP-binding / Lipid-binding / Magnesium / Metal-binding
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 / 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 ...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 / 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 / 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
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
Similarity search - Domain/homology
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of cGAS from Biortus
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Guo, S.
History
DepositionOct 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)85,0982
Polymers85,0982
Non-polymers00
Water21612
1
A: Cyclic GMP-AMP synthase


Theoretical massNumber of molelcules
Total (without water)42,5491
Polymers42,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase


Theoretical massNumber of molelcules
Total (without water)42,5491
Polymers42,5491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.880, 112.049, 59.880
Angle α, β, γ (deg.)90.000, 114.847, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 162 - 520 / Label seq-ID: 4 - 362

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 42549.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Imidazole pH8.0, 16% PEG8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.89 Å / Num. obs: 13050 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 6.4
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2380

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.89 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.813 / SU B: 37.945 / SU ML: 0.644 / Cross valid method: FREE R-VALUE / ESU R Free: 0.68
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3286 597 4.581 %
Rwork0.2744 12434 -
all0.277 --
obs-13031 99.542 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 89.197 Å2
Baniso -1Baniso -2Baniso -3
1--2.348 Å20 Å23.873 Å2
2--3.004 Å20 Å2
3----2.969 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 0 12 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0135436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175370
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.6427288
X-RAY DIFFRACTIONr_angle_other_deg0.9681.58912396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2365634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15922.329292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.431151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4081536
X-RAY DIFFRACTIONr_chiral_restr0.0280.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021256
X-RAY DIFFRACTIONr_nbd_refined0.1460.21036
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1460.24810
X-RAY DIFFRACTIONr_nbtor_refined0.1440.22630
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.211
X-RAY DIFFRACTIONr_nbd_other0.1070.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.140.23
X-RAY DIFFRACTIONr_mcbond_it1.3739.4882572
X-RAY DIFFRACTIONr_mcbond_other1.3739.4882571
X-RAY DIFFRACTIONr_mcangle_it2.52214.2153194
X-RAY DIFFRACTIONr_mcangle_other2.52214.2153195
X-RAY DIFFRACTIONr_scbond_it0.8269.5572864
X-RAY DIFFRACTIONr_scbond_other0.8269.5572862
X-RAY DIFFRACTIONr_scangle_it1.62414.2984094
X-RAY DIFFRACTIONr_scangle_other1.62414.2984094
X-RAY DIFFRACTIONr_lrange_it5.168107.1835928
X-RAY DIFFRACTIONr_lrange_other5.168107.1685927
X-RAY DIFFRACTIONr_ncsr_local_group_10.0610.0510444
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.061160.05009
12BX-RAY DIFFRACTIONLocal ncs0.061160.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.398430.366927X-RAY DIFFRACTION100
3.18-3.2670.372300.351896X-RAY DIFFRACTION100
3.267-3.3620.437360.359889X-RAY DIFFRACTION99.5694
3.362-3.4650.389500.362813X-RAY DIFFRACTION99.424
3.465-3.5780.312370.312821X-RAY DIFFRACTION100
3.578-3.7030.361360.311789X-RAY DIFFRACTION99.8789
3.703-3.8420.309350.292757X-RAY DIFFRACTION98.6301
3.842-3.9980.33380.276764X-RAY DIFFRACTION99.8755
3.998-4.1750.314180.274679X-RAY DIFFRACTION99.8567
4.175-4.3770.283450.272677X-RAY DIFFRACTION99.7238
4.377-4.6130.268300.253668X-RAY DIFFRACTION99.7143
4.613-4.890.325340.241577X-RAY DIFFRACTION99.6737
4.89-5.2250.343290.245568X-RAY DIFFRACTION99.6661
5.225-5.640.318210.272538X-RAY DIFFRACTION98.9381
5.64-6.1720.365370.287472X-RAY DIFFRACTION99.8039
6.172-6.890.394290.308435X-RAY DIFFRACTION99.3576
6.89-7.9360.392250.228401X-RAY DIFFRACTION99.7658
7.936-9.6710.24140.179340X-RAY DIFFRACTION98.6072
9.671-13.4770.156100.155257X-RAY DIFFRACTION98.524
13.477-48.8900.292166X-RAY DIFFRACTION94.8571

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