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

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Basic information

Entry
Database: PDB / ID: 5vdo
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with 2',2'-cGAMP
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 / 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
Chem-1YC / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.218 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 / _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)86,5526
Polymers85,0722
Non-polymers1,4804
Water362
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2763
Polymers42,5361
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2763
Polymers42,5361
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.423, 47.670, 88.861
Angle α, β, γ (deg.)90.000, 110.180, 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 161-522
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-1YC / 2-amino-9-[(1R,3R,6R,8R,9R,11S,14R,16R,17R,18R)-16-(6-amino-9H-purin-9-yl)-3,11,17,18-tetrahydroxy-3,11-dioxido-2,4,7,10,12,15-hexaoxa-3,11-diphosphatricyclo[12.2.1.1~6,9~]octadec-8-yl]-1,9-dihydro-6H-purin-6-one


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
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: 3.218→55.718 Å / Num. obs: 14176 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 75.42 Å2 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.11 / Net I/σ(I): 16.1
Reflection shellResolution: 3.218→3.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2030 / Rpim(I) all: 0.368 / % possible all: 99.5

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Processing

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

4o67


Resolution: 3.218→55.718 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.14
RfactorNum. reflection% reflection
Rfree0.2577 733 5.18 %
Rwork0.2055 --
obs0.2082 14157 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 306.55 Å2 / Biso mean: 104.8982 Å2 / Biso min: 31.35 Å2
Refinement stepCycle: final / Resolution: 3.218→55.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 92 2 5783
Biso mean--128.09 78.61 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025904
X-RAY DIFFRACTIONf_angle_d0.5777966
X-RAY DIFFRACTIONf_chiral_restr0.029879
X-RAY DIFFRACTIONf_plane_restr0.003996
X-RAY DIFFRACTIONf_dihedral_angle_d12.5822182
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3287X-RAY DIFFRACTION6.744TORSIONAL
12B3287X-RAY DIFFRACTION6.744TORSIONAL
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 (%)
3.218-3.46640.3781330.27652637277099
3.4664-3.81520.25471580.220426562814100
3.8152-4.36710.26831330.195326892822100
4.3671-5.50130.23381540.18626692823100
5.5013-55.72640.2421550.1982773292899
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)
13.81611.1554.39834.1641.63165.40111.85680.8612-1.722-0.0119-1.0049-0.76580.82821.0871-0.93151.12530.0291-0.09360.75810.28010.6022-29.1731-2.9216-23.548
28.42935.39786.52798.5185.06875.2513-1.29-1.32750.748-0.7622-0.12560.33151.47160.86041.3931.09-0.32090.22361.85270.04651.1369-22.013.992-20.6852
34.7226-2.09940.10269.21021.88163.39720.188-0.0203-0.0693-0.38390.1047-1.7912-0.43441.574-0.38170.7126-0.34160.03481.78540.30241.1665-12.282916.6646-20.5952
43.2771-3.5185-3.84384.48144.41774.95090.09660.30930.128-1.1047-0.1983-0.3795-0.34840.31420.14851.1134-0.03610.05270.90080.09170.6469-20.291611.2474-23.7312
53.45081.0819-2.27634.9535-1.64566.6563-0.0003-0.274-0.34310.1362-0.2129-0.6711-0.50490.69260.09620.6518-0.12020.01160.4792-0.04690.4505-31.965715.4682-12.1895
65.61540.42280.12553.4351-0.46226.28040.00820.51250.1292-0.34710.07440.0130.05030.4579-0.08990.7016-0.10590.00820.37260.02140.2692-43.397115.3168-26.1616
76.79730.2177-1.45774.51671.08325.10590.22720.12180.5647-0.25260.0116-1.738-0.51751.7035-0.31770.7427-0.00880.14551.07770.21680.8907-20.07615.659519.4481
88.4369-6.201-3.05625.48674.80628.3042-0.2886-1.88640.65161.00981.0053-1.7003-0.17311.6411-0.70411.0284-0.0998-0.22822.0633-0.07281.3598-13.99769.727729.5226
93.493-0.2581-0.09343.5062-1.27586.4068-0.0465-0.2161-0.11630.134-0.0128-0.44690.13170.59010.01970.58420.0657-0.00360.33930.00080.3813-38.5364-0.195520.4228
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 298 )A225 - 298
4X-RAY DIFFRACTION4chain 'A' and (resid 299 through 334 )A299 - 334
5X-RAY DIFFRACTION5chain 'A' and (resid 335 through 405 )A335 - 405
6X-RAY DIFFRACTION6chain 'A' and (resid 406 through 521 )A406 - 521
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 272 )B160 - 272
8X-RAY DIFFRACTION8chain 'B' and (resid 273 through 325 )B273 - 325
9X-RAY DIFFRACTION9chain 'B' and (resid 326 through 521 )B326 - 521

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