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- PDB-7fu7: Crystal Structure of human cyclic GMP-AMP synthase -

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Basic information

Entry
Database: PDB / ID: 7fu7
TitleCrystal Structure of human cyclic GMP-AMP synthase
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / CYCLIC GMP-AMP SYNTHASE / CGAS / DNA-BINDING / ACTIVATOR DNA / PATTERN RECOGNITION RECEPTOR / INNATE IMMUNE RESPONSE / VIRAL DNA RECOGNITION
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 / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
: / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLeibrock, L. / Benz, J. / Groebke-Zbinden, K. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human cyclic GMP-AMP synthase complex
Authors: Groebke-Zbinden, K. / Vandemeulebroucke, A. / Hilbert, M. / Rudolph, M.G.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8623
Polymers42,4051
Non-polymers4572
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.015, 59.359, 162.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Cyclic GMP-AMP synthase / cGAMP synthase / cGAS / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 42404.906 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 161-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Plasmid: pET21a_cGAS(161-522_wt) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YNW / (6M)-2-(benzylamino)-6-(2-chloro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid


Mass: 391.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18ClN3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of ...Details: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99983 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99983 Å / Relative weight: 1
ReflectionResolution: 2.25→59.36 Å / Num. obs: 21454 / % possible obs: 99.9 % / Redundancy: 6.528 % / Biso Wilson estimate: 70.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.04 / Χ2: 0.876 / Net I/σ(I): 19.95 / Num. measured all: 140049 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.316.9142.0080.8610640153915390.3582.169100
2.31-2.376.8331.461.1710455153115300.5481.57899.9
2.37-2.446.8031.1881.459905145614560.6771.284100
2.44-2.526.6650.8452.149658144914490.7570.915100
2.52-2.66.5990.5713.139073137813750.8750.61999.8
2.6-2.696.1570.3994.198361135913580.9350.43799.9
2.69-2.796.6990.2995.898762130813080.9650.324100
2.79-2.96.8380.218.578541125212490.9860.22899.8
2.9-3.036.7440.14312.518221122012190.990.15599.9
3.03-3.186.7160.10116.947770115811570.9950.1199.9
3.18-3.356.4780.06923.887145110411030.9970.07599.9
3.35-3.566.0260.04830.486375105910580.9980.05299.9
3.56-3.86.7150.03841.1566219889860.9990.04299.8
3.8-4.116.6350.03147.5762379419400.9990.03499.9
4.11-4.56.4720.02655.08557986286210.028100
4.5-5.035.9310.02454.29465078478410.026100
5.03-5.815.9960.02455.58418569969810.02699.9
5.81-7.126.1530.02457.5737046046020.9990.02699.7
7.12-10.065.3890.02161.5626194894860.9990.02399.4
10.06-59.365.2470.0226515483042950.9990.02497

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.24→59.36 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.6 / Stereochemistry target values: ML
Details: phenyl group appears less defined by electron density than rest of ligand;
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 953 5.03 %RANDOM
Rwork0.2227 18011 --
obs0.2238 18964 87.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.9 Å2 / Biso mean: 98.7999 Å2 / Biso min: 43.17 Å2
Refinement stepCycle: final / Resolution: 2.24→59.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 29 27 2924
Biso mean--68.69 70.56 -
Num. residues----347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.360.4418410.374474778826
2.36-2.510.3461220.33322464258685
2.51-2.70.311630.306128773040100
2.7-2.970.35451570.309829153072100
2.97-3.40.26581700.262928943064100
3.4-4.290.26391550.2129763131100
4.29-59.360.19511450.191531383283100
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)
13.42570.65630.53857.569-0.8622.6021-0.0657-0.87410.83920.1991-0.11251.61540.4039-0.8907-0.37030.7017-0.1585-0.04411.0057-0.07040.7976-9.886817.66625.1413
24.003-1.54471.40175.45131.7794.94390.1556-0.24451.08580.2878-0.1591-0.6934-0.59820.19910.12960.6642-0.1203-0.14670.6798-0.08461.07659.129830.38820.1154
34.58220.92611.35523.96030.24222.9286-0.0622-0.74271.2450.4142-0.1087-0.2627-0.59760.1363-0.26530.4882-0.0465-0.12740.6067-0.12630.61994.944326.288421.5181
44.95290.82761.71283.91520.4576.42740.5049-0.8273-0.36530.7616-0.1825-0.23171.20850.0417-0.50440.5910.049-0.05260.54330.07970.42376.84766.008723.2366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 198 )A161 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 272 )A199 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 361 )A273 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 522 )A362 - 522

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