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- PDB-5vds: Human cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdUMP -

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Basic information

Entry
Database: PDB / ID: 5vds
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdUMP
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / STING / cGAMP
Function / homology
Function and homology information


2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / 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 / regulation of T cell activation / pattern recognition receptor signaling pathway / : ...2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / 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 / regulation of T cell activation / pattern recognition receptor signaling pathway / : / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / 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 / 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 / nucleoplasm / ATP binding / metal ion binding / nucleus / 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 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / 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 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3',3'-cdUMP / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.766 Å
AuthorsByrnes, L.J. / Hall, J.D.
CitationJournal: Protein Sci. / Year: 2017
Title: The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition.
Authors: Hall, J. / Ralph, E.C. / Shanker, S. / Wang, H. / Byrnes, L.J. / Horst, R. / Wong, J. / Brault, A. / Dumlao, D. / Smith, J.F. / Dakin, L.A. / Schmitt, D.C. / Trujillo, J. / Vincent, F. / ...Authors: Hall, J. / Ralph, E.C. / Shanker, S. / Wang, H. / Byrnes, L.J. / Horst, R. / Wong, J. / Brault, A. / Dumlao, D. / Smith, J.F. / Dakin, L.A. / Schmitt, D.C. / Trujillo, J. / Vincent, F. / Griffor, M. / Aulabaugh, A.E.
History
DepositionApr 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.Rmerge_I_obs
Revision 1.4Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4326
Polymers85,0722
Non-polymers1,3604
Water1,62190
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2163
Polymers42,5361
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2163
Polymers42,5361
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.450, 48.408, 86.086
Angle α, β, γ (deg.)90.000, 104.810, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 160 - 521 / Label seq-ID: 1 - 362

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

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


Mass: 42536.102 Da / Num. of mol.: 2 / Fragment: UNP residues 161-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MB21D1, C6orf150 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9BJ / 3',3'-cdUMP / 1-{(2R,6R,8R,10aR,12R,13R,13aS)-6-[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-1,2-dihydroxyethyl]-2,8,13-trihydroxy-2,8-dioxohexahydro-2H,4H,8H,10H-2lambda~5~,8lambda~5~-furo[3,2-d][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-12-yl}pyrimidine-2,4(1H,3H)-dione


Mass: 614.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24N4O16P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 18-20% PEG 3350, 0.2 M ammonium citrate pH 7

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.766→58.165 Å / Num. obs: 22387 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.12 / Net I/σ(I): 10.8
Reflection shellHighest resolution: 2.766 Å / Rmerge(I) obs: 0.764 / Rpim(I) all: 0.51

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Processing

Software
NameVersionClassification
PHENIXdev_1999refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O67

4o67


Resolution: 2.766→58.165 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 1132 5.06 %
Rwork0.206 21241 -
obs0.208 22373 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.23 Å2 / Biso mean: 53.5442 Å2 / Biso min: 7.75 Å2
Refinement stepCycle: final / Resolution: 2.766→58.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 82 90 5674
Biso mean--59.26 30.93 -
Num. residues----685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025530
X-RAY DIFFRACTIONf_angle_d0.5367712
X-RAY DIFFRACTIONf_chiral_restr0.028861
X-RAY DIFFRACTIONf_plane_restr0.002953
X-RAY DIFFRACTIONf_dihedral_angle_d11.8322128
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3212X-RAY DIFFRACTION7.094TORSIONAL
12B3212X-RAY DIFFRACTION7.094TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7662-2.89210.31351380.279726252763
2.8921-3.04460.31821400.25826312771
3.0446-3.23530.30031290.232326452774
3.2353-3.48510.29131360.226826312767
3.4851-3.83570.24541470.202926232770
3.8357-4.39060.26061440.182426672811
4.3906-5.5310.19081490.172126632812
5.531-58.17780.19261490.190727562905
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)
16.19840.275-1.01130.04130.03160.34180.0621-0.30321.66460.1317-0.0739-0.3818-0.42010.5145-0.14220.4352-0.1321-0.05060.50690.0320.9828-29.115220.315422.6281
25.1385-0.5903-4.80970.1180.53654.5071-0.2591.12010.78440.23470.1533-0.0628-0.6659-0.9543-0.00530.52470.0457-0.09651.24140.21681.1481-21.531613.536519.8851
32.0979-0.03750.28911.3501-0.05031.3875-0.13110.10420.1820.1730.2143-0.7713-0.08260.7516-0.05230.27870.0573-0.12110.88540.13860.9747-11.2362-0.268317.9972
41.5306-1.2113-1.23414.09210.42772.43470.1131-0.61330.42721.24670.023-0.6433-0.2840.7686-0.05730.5777-0.2053-0.12050.7251-0.04350.6126-16.2313.288727.0892
55.2727-1.70271.03952.5574-1.0533.24380.0216-0.0760.2363-0.0471-0.0907-0.4928-0.07170.34870.04360.1772-0.04410.02890.1929-0.00720.3009-31.25082.21629.6077
66.07630.2382-0.74074.60752.25634.5248-0.2057-0.58870.05370.73870.0372-0.5775-0.08030.55850.18380.2464-0.0535-0.05160.2153-0.02230.2328-38.39096.173531.0153
73.2823-0.3187-0.13822.8793-0.11294.45740.064-0.3483-0.02570.14570.0513-0.2040.11450.077-0.07390.1636-0.0388-0.03910.12460.00290.1658-42.9115-0.530824.4283
83.2162.78671.06132.76461.2161.48580.3127-0.2877-1.7250.1823-0.1076-0.37720.46920.2798-0.20760.61770.0266-0.01380.27740.09760.3737-31.041-1.5008-23.3951
92.77830.9998-0.70881.88480.18321.31780.1066-0.07490.31280.0844-0.0836-0.53390.03310.4021-0.02880.2542-0.0503-0.06090.54440.07730.7141-18.726417.3026-18.9652
102.75880.1706-0.56422.65670.23952.3310.18730.15730.2261-0.18080.1079-0.53240.05780.5604-0.31840.19950.0523-0.07240.36690.05240.3251-22.033413.5942-19.3595
111.7821-0.19970.53251.13180.02042.79050.04990.1690.0166-0.2063-0.0671-0.19530.0889-0.0192-0.01070.19740.02490.05520.11850.01610.2142-42.460815.0352-23.2069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 199 )A160 - 199
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 224 )A200 - 224
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 288 )A225 - 288
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 326 )A289 - 326
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 405 )A327 - 405
6X-RAY DIFFRACTION6chain 'A' and (resid 406 through 434 )A406 - 434
7X-RAY DIFFRACTION7chain 'A' and (resid 435 through 521 )A435 - 521
8X-RAY DIFFRACTION8chain 'B' and (resid 160 through 199 )B160 - 199
9X-RAY DIFFRACTION9chain 'B' and (resid 200 through 272 )B200 - 272
10X-RAY DIFFRACTION10chain 'B' and (resid 273 through 361 )B273 - 361
11X-RAY DIFFRACTION11chain 'B' and (resid 362 through 521 )B362 - 521

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