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- PDB-4km5: X-ray crystal structure of human cyclic GMP-AMP synthase (cGAS) -

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Basic information

Entry
Database: PDB / ID: 4km5
TitleX-ray crystal structure of human cyclic GMP-AMP synthase (cGAS)
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / DNA Sensor / Innate Immunity / Zinc Finger / Nucleotidyl Transferase / DNA / Cytoplasmic
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 / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of double-strand break repair via homologous recombination ...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 / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / cAMP-mediated signaling / nucleosome binding / positive regulation of type I interferon production / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / 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 / 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-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
Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.499 Å
AuthorsKranzusch, P.J. / Lee, A.S.Y. / Berger, J.M. / Doudna, J.A.
CitationJournal: Cell Rep / Year: 2013
Title: Structure of Human cGAS Reveals a Conserved Family of Second-Messenger Enzymes in Innate Immunity.
Authors: Kranzusch, P.J. / Lee, A.S. / Berger, J.M. / Doudna, J.A.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0562
Polymers42,9901
Non-polymers651
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.454, 162.700, 58.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cyclic GMP-AMP synthase / / cGAMP synthase / cGAS / h-cGAS / Mab-21 domain-containing protein 1


Mass: 42990.473 Da / Num. of mol.: 1 / Fragment: UNP residues 157-522
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, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 52.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.044M potassium chloride, 0.01M magnesium chloride, 0.025M Tris pH 7.0, 0.015M Tris pH 9.0, 6.9% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
22911
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-211.2818
SYNCHROTRONALS 8.3.120.9792
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELMar 6, 2013
ADSC QUANTUM 315r2CCDFeb 3, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28181
20.97921
ReflectionResolution: 2.499→47.445 Å / Num. all: 29674 / Num. obs: 16035 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameClassification
Web-Icedata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.499→47.445 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 800 5.01 %
Rwork0.2245 --
obs0.2253 15977 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.499→47.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 1 36 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033040
X-RAY DIFFRACTIONf_angle_d0.6614077
X-RAY DIFFRACTIONf_dihedral_angle_d14.7261177
X-RAY DIFFRACTIONf_chiral_restr0.054439
X-RAY DIFFRACTIONf_plane_restr0.003519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4985-2.65510.36931280.32532439X-RAY DIFFRACTION98
2.6551-2.860.33631310.28832490X-RAY DIFFRACTION100
2.86-3.14780.29261330.26772492X-RAY DIFFRACTION100
3.1478-3.60310.31241330.24972528X-RAY DIFFRACTION100
3.6031-4.5390.22111330.20562541X-RAY DIFFRACTION100
4.539-47.45340.19231420.20212687X-RAY DIFFRACTION100
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)
11.2623-0.26910.87081.85990.05089.396-0.0604-0.2343-0.1566-0.41940.3030.65840.0857-1.2834-0.34560.5346-0.0561-0.08610.65690.07990.9384-10.852356.285617.4548
23.51-0.7198-2.48563.1542-1.09685.52690.1384-0.55470.05170.2780.0623-0.16160.00750.5805-0.07940.60910.0541-0.14330.6083-0.00350.60688.040659.683932.133
31.9792-0.1714-0.39223.7407-1.55444.0392-0.0056-0.3721-0.14060.08010.16290.0720.40720.1245-0.17350.52460.0275-0.06710.5121-0.05580.55673.502860.328823.1502
42.8814-0.28030.29083.71050.92573.52830.42780.4038-0.3033-0.7793-0.2090.01040.90150.1756-0.20310.80380.0485-0.13170.4135-0.03220.47587.933655.63693.5916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 199 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 272 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 405 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 522 )A0

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