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

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Basic information

Entry
Database: PDB / ID: 5vdr
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdIMP
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
3',3'-cdIMP / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.042 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)87,8458
Polymers85,0722
Non-polymers2,7726
Water57632
1
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2623
Polymers42,5361
Non-polymers7262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5835
Polymers42,5361
Non-polymers2,0474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.528, 48.395, 89.099
Angle α, β, γ (deg.)90.000, 109.890, 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 161-521
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-9B7 / 3',3'-cdIMP / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-3,5,10,12-tetrahydroxy-2,9-bis(6-oxo-3,6-dihydro-9H-purin-9-yl)octahydro-2H,5H, 7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-5,12-dione


Mass: 660.381 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
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: 3.04→55.901 Å / Num. obs: 16476 / % possible obs: 96.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 65.99 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.095 / Net I/σ(I): 11.1
Reflection shellHighest resolution: 3.04 Å / Rmerge(I) obs: 0.491 / Rpim(I) all: 0.463

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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: 3.042→55.901 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.91
RfactorNum. reflection% reflection
Rfree0.2535 757 4.6 %
Rwork0.2083 --
obs0.2104 16454 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 253.79 Å2 / Biso mean: 84.0409 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 3.042→55.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5641 0 178 32 5851
Biso mean--97.98 48.54 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025953
X-RAY DIFFRACTIONf_angle_d0.6048053
X-RAY DIFFRACTIONf_chiral_restr0.03891
X-RAY DIFFRACTIONf_plane_restr0.003989
X-RAY DIFFRACTIONf_dihedral_angle_d13.5442157
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3252X-RAY DIFFRACTION5.477TORSIONAL
12B3252X-RAY DIFFRACTION5.477TORSIONAL
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 (%)
3.0421-3.2770.32191530.28432013354100
3.277-3.60670.29151550.2493060321596
3.6067-4.12850.30621370.21442879301690
4.1285-5.20090.22841510.1832603411100
5.2009-55.91020.2141610.19013297345898
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)
14.7977-0.35070.58590.2064-0.260.33440.69990.12151.16270.411-0.8419-0.9112-0.33820.74270.11370.5179-0.08140.05450.9562-0.02191.4132-30.780219.320224.4666
20.1029-0.1157-0.370.30870.85452.45250.0683-0.13530.28080.0052-0.3235-0.8828-0.34560.33090.2870.76030.0717-0.00131.23410.22931.4318-20.098611.640220.934
32.56360.71010.12773.6457-0.53051.29320.00120.00740.1702-0.0613-0.0276-1.16140.42480.93020.06610.61610.22930.0331.1620.17181.049-13.4148-6.111516.9858
40.2198-0.5303-1.12642.1663.75496.98170.0889-0.39050.6161.1829-0.7004-1.0810.16580.58760.49040.7817-0.0612-0.19961.1360.25411.1041-11.93138.252331.5028
52.4556-0.1607-0.52532.155-0.69663.49150.1282-0.0323-0.0013-0.0994-0.1113-0.2114-0.13840.44540.01680.4169-0.00640.00240.35960.00950.2441-35.63892.606618.4647
63.62780.1284-0.85681.6832-0.06184.65390.0282-0.434-0.06330.15560.1370.3075-0.05320.1717-0.08140.45070.0737-0.02620.3491-0.0120.3061-42.5085-3.921129.66
72.1675-0.0311.35272.01550.42320.93190.52330.6176-1.068-0.0689-0.3472-0.22440.47280.4065-0.09180.63080.0162-0.13230.60090.07110.5536-31.3252-3.4442-24.0044
81.0617-1.1009-0.81894.688-0.30411.6218-0.1308-0.3162-0.24150.3350.323-1.2467-0.07840.7778-0.2510.6648-0.1715-0.17841.048-0.04020.9821-13.469517.7358-17.5733
92.87732.22631.344.31012.49795.08440.29810.3186-0.8576-0.89410.0111-1.6493-0.32480.3463-0.16740.5830.07530.16960.68720.00580.9802-14.82746.6062-29.6531
103.9623-0.3026-1.48352.9069-0.47183.652-0.0148-0.0682-0.01560.06170.0123-0.2504-0.06120.3068-0.10040.3717-0.0282-0.07550.31060.01220.2552-30.570616.3033-11.7801
114.1843-0.03231.09513.4523-0.7444.14960.1050.36110.1357-0.26960.07830.2583-0.11030.1411-0.16470.3693-0.01950.00750.26920.00960.2385-43.009415.5296-25.9832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 160 through 197 )A160 - 197
2X-RAY DIFFRACTION2chain 'A' and (resid 198 through 224 )A198 - 224
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 272 )A225 - 272
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 306 )A273 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 476 )A307 - 476
6X-RAY DIFFRACTION6chain 'A' and (resid 477 through 521 )A477 - 521
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 197 )B160 - 197
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 272 )B198 - 272
9X-RAY DIFFRACTION9chain 'B' and (resid 273 through 326 )B273 - 326
10X-RAY DIFFRACTION10chain 'B' and (resid 327 through 405 )B327 - 405
11X-RAY DIFFRACTION11chain 'B' and (resid 406 through 521 )B406 - 521

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