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- PDB-5vdq: Human cyclic GMP-AMP synthase (cGAS) in complex with 2',5'-GpAp -

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Basic information

Entry
Database: PDB / ID: 5vdq
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with 2',5'-GpAp
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 / cGMP-mediated signaling ...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 / cGMP-mediated signaling / 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 / cAMP-mediated signaling / 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 / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
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
2',5'-GpAp / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.246 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 1.3Oct 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
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
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5886
Polymers85,0722
Non-polymers1,5164
Water00
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2943
Polymers42,5361
Non-polymers7582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2943
Polymers42,5361
Non-polymers7582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.211, 47.632, 88.365
Angle α, β, γ (deg.)90.000, 110.050, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0

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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 161-522
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-9BG / 2',5'-GpAp / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate


Mass: 692.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O14P2

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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: 2.51 Å3/Da / Density % sol: 50.98 %
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: 3.246→55.492 Å / Num. obs: 13619 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 75.12 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.085 / Net I/σ(I): 11.1
Reflection shellHighest resolution: 3.24 Å / Rmerge(I) obs: 0.502 / Rpim(I) all: 0.484

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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: 3.246→55.492 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 652 4.79 %
Rwork0.2083 12947 -
obs0.211 13599 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.95 Å2 / Biso mean: 90.7826 Å2 / Biso min: 29.35 Å2
Refinement stepCycle: final / Resolution: 3.246→55.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 94 0 5773
Biso mean--112.81 --
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035894
X-RAY DIFFRACTIONf_angle_d0.6777949
X-RAY DIFFRACTIONf_chiral_restr0.033876
X-RAY DIFFRACTIONf_plane_restr0.003994
X-RAY DIFFRACTIONf_dihedral_angle_d13.2582177
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3338X-RAY DIFFRACTION6.398TORSIONAL
12B3338X-RAY DIFFRACTION6.398TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2456-3.49620.38691420.304225432685100
3.4962-3.84790.29151290.241725652694100
3.8479-4.40450.25271210.19742589271099
4.4045-5.54840.24311220.1812596271899
5.5484-55.50020.23551380.18932654279298
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)
12.36851.61841.84573.58441.80971.56990.68230.4823-1.56250.2403-0.3505-0.50910.53260.425-0.26110.8220.0778-0.02250.56120.16950.6432-29.1993-26.5321-23.634
21.8265-2.8579-0.73145.79520.4673.3647-0.0788-0.10250.2974-0.0809-0.0307-1.2465-0.39280.82590.08920.5291-0.1284-0.1310.80810.10340.7759-15.7941-7.2803-17.4509
35.3782-1.8948-2.0572.52981.24076.29680.1179-0.3271-0.0141-0.2179-0.2482-0.3708-0.39920.76170.09740.5888-0.0644-0.03360.50680.04330.5456-21.6438-9.7256-20.0164
44.71240.69260.99583.4875-1.08265.87190.01460.1829-0.041-0.12640.12040.22160.0005-0.0723-0.11570.5095-0.020.04330.2967-0.04080.3141-43.1431-9.7867-23.8925
54.5193-0.95960.04871.66490.07921.02550.17720.62211.1465-0.1526-0.2162-0.7428-0.30840.59250.05850.61290.03030.12760.9270.17671.0472-23.6025-14.16620.7964
65.13271.12641.61454.39290.37993.66270.0219-0.10510.02440.4555-0.4505-1.06090.42881.00020.29270.65210.07340.01670.95310.20510.6884-19.3571-23.518819.8873
73.6123-0.7148-0.78622.961-1.09927.5360.0496-0.0386-0.08070.07640.17740.2279-0.04310.106-0.21960.43440.0113-0.00730.40790.02570.356-43.4936-21.994123.9181
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 272 )A200 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 388 )A273 - 388
4X-RAY DIFFRACTION4chain 'A' and (resid 389 through 521 )A389 - 521
5X-RAY DIFFRACTION5chain 'B' and (resid 160 through 248 )B160 - 248
6X-RAY DIFFRACTION6chain 'B' and (resid 249 through 388 )B249 - 388
7X-RAY DIFFRACTION7chain 'B' and (resid 389 through 521 )B389 - 521

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