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

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Basic information

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


water channel activity / plasma membrane
Similarity search - Function
Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Mab-21 protein nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like ...Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Mab-21 protein nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4BW / Probable aquaporin AqpM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.576 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Water2,630146
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)213.896, 47.975, 88.274
Angle α, β, γ (deg.)90.000, 110.070, 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-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


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.: 146 / 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: 2.51 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: 2.576→55.306 Å / Num. obs: 26726 / % possible obs: 98.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.07 Å2 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.1 / Net I/σ(I): 14.8
Reflection shellHighest resolution: 2.576 Å / Rmerge(I) obs: 0.558 / Rpim(I) all: 0.531

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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: 2.576→55.306 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1333 4.99 %
Rwork0.202 25364 -
obs0.2038 26697 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.82 Å2 / Biso mean: 64.3928 Å2 / Biso min: 18.96 Å2
Refinement stepCycle: final / Resolution: 2.576→55.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5685 0 92 146 5923
Biso mean--44.29 46.56 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035909
X-RAY DIFFRACTIONf_angle_d0.6477972
X-RAY DIFFRACTIONf_chiral_restr0.034879
X-RAY DIFFRACTIONf_plane_restr0.002996
X-RAY DIFFRACTIONf_dihedral_angle_d13.0562190
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3354X-RAY DIFFRACTION7.012TORSIONAL
12B3354X-RAY DIFFRACTION7.012TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5761-2.66820.34551210.30462542266399
2.6682-2.7750.33241210.26812516263799
2.775-2.90130.30931490.265825322681100
2.9013-3.05430.34571220.253325892711100
3.0543-3.24560.26941400.229325362676100
3.2456-3.49620.25431130.2282513262697
3.4962-3.84790.25061390.18872319245891
3.8479-4.40450.21981300.17812559268999
4.4045-5.54840.17521470.161425842731100
5.5484-55.31850.19841510.175826742825100
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)
12.48092.0481-0.7023.56330.57560.9154-0.1198-0.6133-0.8044-0.033-0.105-0.46270.11510.05270.21560.56860.032-0.04460.41690.0930.3844-28.5075-2.4526-23.6531
22.0519-2.0251-0.90144.44370.47183.5028-0.0667-0.4910.26180.4195-0.0676-0.9517-0.20310.67080.08220.4119-0.0913-0.08630.67750.10490.6543-15.475816.9119-17.5287
33.1912-0.0983-2.11662.4197-0.10933.80250.12360.0166-0.00390.0033-0.0767-0.4783-0.13050.3188-0.06570.35170.0008-0.08850.42150.02450.3863-24.397813.0504-18.3663
43.62230.40960.80283.0179-0.35745.9114-0.05170.1405-0.092-0.23590.06270.0381-0.02990.1062-0.00010.28530.03950.01850.2305-0.0170.246-42.690215.4016-26.1149
52.6864-3.047-1.1953.50121.17231.08650.5167-0.13741.23850.2285-0.3454-1.0808-0.43630.5598-0.19690.5656-0.0460.0270.64480.21560.8633-29.287219.187523.8093
64.04321.2480.7046.5814-0.02231.0206-0.11830.5462-0.0352-0.1039-0.0135-1.08910.20020.58910.06420.48240.15550.07730.95410.20870.7329-13.9115-2.406217.2145
74.04070.39372.16293.62890.13644.10330.1257-0.3610.24270.3548-0.3841-0.81030.22020.47020.13580.3986-0.01860.01530.65580.09570.529-21.63491.941820.3476
81.44860.188-1.24771.5857-0.11486.06930.0589-0.04130.09060.06530.04270.034-0.0366-0.0687-0.08770.2949-0.0003-0.02180.311-0.01030.3104-43.27872.060423.7127
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 405 )A273 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 521 )A406 - 521
5X-RAY DIFFRACTION5chain 'B' and (resid 160 through 199 )B160 - 199
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 272 )B200 - 272
7X-RAY DIFFRACTION7chain 'B' and (resid 273 through 388 )B273 - 388
8X-RAY DIFFRACTION8chain 'B' and (resid 389 through 521 )B389 - 521

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