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- PDB-5vdu: Human cyclic GMP-AMP synthase (cGAS) in complex with Compound F2 -

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Basic information

Entry
Database: PDB / ID: 5vdu
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with Compound F2
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / STING / cGAMP
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
2-(pyridin-2-yl)pyrimidine / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.729 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 / 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

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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)85,8328
Polymers85,0722
Non-polymers7606
Water93752
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7593
Polymers42,5361
Non-polymers2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0735
Polymers42,5361
Non-polymers5374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.415, 48.019, 86.466
Angle α, β, γ (deg.)90.000, 104.940, 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: ZN / End label comp-ID: ZN / Auth seq-ID: 160 - 601 / Label seq-ID: 1

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

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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-9BS / 2-(pyridin-2-yl)pyrimidine


Mass: 157.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
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: 2.729→52.274 Å / Num. obs: 22940 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 46.77 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.078 / Rrim(I) all: 0.143 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
2.73-2.883.40.69233650.6960.4370.8299.6
8.63-83.543.10.0270.9980.0180.03395.6

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHENIXdev_1999refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O67

4o67


Resolution: 2.729→52.274 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2521 1061 4.63 %
Rwork0.2223 --
obs0.2237 22914 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 229.12 Å2 / Biso mean: 65.174 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 2.729→52.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 98 52 5724
Biso mean--80.37 37.31 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025708
X-RAY DIFFRACTIONf_angle_d0.6657843
X-RAY DIFFRACTIONf_chiral_restr0.03870
X-RAY DIFFRACTIONf_plane_restr0.0031099
X-RAY DIFFRACTIONf_dihedral_angle_d12.392158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3326X-RAY DIFFRACTION7.344TORSIONAL
12B3326X-RAY DIFFRACTION7.344TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7287-2.85290.36691200.32532774289499
2.8529-3.00330.31921440.28212750289499
3.0033-3.19140.27811380.2642701283999
3.1914-3.43780.2841350.25882732286799
3.4378-3.78370.3011110.23192674278597
3.7837-4.3310.22591220.19842690281296
4.331-5.45560.22561410.18042724286598
5.4556-52.28390.20651500.19282808295897
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)
14.41150.21440.62712.07020.50361.56270.23590.1582-0.2167-0.0466-0.2151-0.30470.30930.5628-0.01250.4730.07750.00610.5260.08810.2471-25.98087.7507-21.1454
25.25322.16312.98595.46724.18046.02620.1960.4877-0.2579-0.1549-0.0727-1.2920.35771.1049-0.39410.34160.0850.14770.96480.23060.6214-9.702213.0036-25.745
32.82230.0731-0.95860.93510.02324.02110.02630.070.06140.16-0.08860.0241-0.06120.47240.00340.27780.0335-0.06480.33090.03830.2511-30.401214.0892-14.4197
42.2891-0.37850.48882.7578-0.49424.17990.0180.2872-0.0345-0.20520.0274-0.1350.06030.0533-0.04560.29180.00680.05080.1984-0.02640.1977-44.93615.1102-26.1604
58.7604-0.7321-1.5390.48290.11230.8890.13050.09950.6468-0.1747-0.1599-0.355-0.36960.3737-0.04990.5655-0.12030.06320.63240.02730.7218-26.961816.57421.078
66.70562.17190.59836.9019-1.82652.89230.01570.6331-0.5137-0.0948-0.0822-1.01070.20440.92020.0890.37770.15270.0730.72260.01670.6769-12.8807-4.43115.4286
72.9268-3.4115-2.04167.10624.03882.7281-0.1502-0.30160.98630.5870.4295-1.0757-0.58031.1737-0.02610.5811-0.1883-0.10170.8041-0.03990.7547-12.69311.431826.7653
85.79-1.95860.70562.9667-0.4214.2941-0.0008-0.05780.1071-0.10230.0309-0.29740.10040.4772-0.10970.3249-0.05670.05640.23620.00780.2724-31.12240.593710.5015
95.31910.6003-1.41694.35513.03513.8834-0.0555-0.91110.0550.8965-0.0011-0.4758-0.63870.48040.02210.3345-0.1059-0.06890.3229-0.02390.2821-38.61695.542531.1124
102.8296-0.0538-1.21432.3111-0.23265.64340.0229-0.2006-0.0874-0.0080.0281-0.02010.10870.1833-0.07350.2791-0.0287-0.01180.1697-0.00260.2293-43.2939-1.400424.0481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 253 )A160 - 253
2X-RAY DIFFRACTION2chain 'A' and (resid 254 through 307 )A254 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 405 )A308 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 520 )A406 - 520
5X-RAY DIFFRACTION5chain 'B' and (resid 160 through 224 )B160 - 224
6X-RAY DIFFRACTION6chain 'B' and (resid 225 through 272 )B225 - 272
7X-RAY DIFFRACTION7chain 'B' and (resid 273 through 326 )B273 - 326
8X-RAY DIFFRACTION8chain 'B' and (resid 327 through 405 )B327 - 405
9X-RAY DIFFRACTION9chain 'B' and (resid 406 through 434 )B406 - 434
10X-RAY DIFFRACTION10chain 'B' and (resid 435 through 520 )B435 - 520

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