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- PDB-7fti: Crystal Structure of human cyclic GMP-AMP synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7fti
TitleCrystal Structure of human cyclic GMP-AMP synthase in complex with 5-(4-fluorophenyl)-2-methylpyrazole-3-carboxylic acid
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE RESPONSE / NTASE / DNA SENSOR
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
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 Å
AuthorsLeibrock, L. / Benz, J. / Groebke-Zbinden, K. / Brunner, M. / 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

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6913
Polymers42,4051
Non-polymers2862
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.050, 44.710, 59.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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
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-YMI / 3-(4-fluorophenyl)-1-methyl-1H-pyrazole-5-carboxylic acid


Mass: 220.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.11 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→82.02 Å / Num. obs: 29826 / % possible obs: 98 % / Redundancy: 6.872 % / Biso Wilson estimate: 41.04 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 0.864 / Net I/σ(I): 16.6 / Num. measured all: 204969 / Scaling rejects: 3693
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
2-2.056.4551.9380.8414317221822180.2092.111100
2.05-2.117.0151.3181.3715006213921390.4281.424100
2.11-2.177.1331.1431.6514815207720770.5711.233100
2.17-2.246.9822.5961.3512352206817690.6052.81285.5
2.24-2.316.0380.3937.1310059195616660.980.43485.2
2.31-2.397.230.5323.8414012193819380.8350.574100
2.39-2.486.8140.3834.8312694186318630.9020.415100
2.48-2.586.8780.2976.3312106176017600.9460.322100
2.58-2.77.4960.2258.8512916172317230.9770.242100
2.7-2.837.6050.17311.4312548165016500.9850.186100
2.83-2.987.4830.12116.2111868158615860.990.13100
2.98-3.167.3220.08223.1610763147014700.9960.088100
3.16-3.386.9330.06130.379678139613960.9980.066100
3.38-3.656.0370.04834.997890131013070.9980.05399.8
3.65-45.7460.04240.436953122512100.9980.04698.8
4-4.477.1240.03251.467972112011190.9990.03599.9
4.47-5.166.7630.02952.9566219799790.9990.032100
5.16-6.326.5830.02752.4956558608590.9990.0399.9
6.32-8.946.020.02452.4741246856850.9990.026100
8.94-82.036.3590.01757.47262041541210.01999.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2→82.03 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.198
Details: ligand well defined by electron density. 19F library NMR fragment hit
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1258 4.94 %RANDOM
Rwork0.227 ---
obs0.229 25484 83.8 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 188.01 Å2 / Biso mean: 63.06 Å2 / Biso min: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.4328 Å20 Å20 Å2
2---0.7707 Å20 Å2
3----0.6621 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2→82.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 17 73 3004
Biso mean--47.06 45.98 -
Num. residues----354
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1109SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes495HARMONIC5
X-RAY DIFFRACTIONt_it2988HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3354SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2988HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4008HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion20.32
LS refinement shellResolution: 2→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.4377 63 5.08 %
Rwork0.4111 1178 -
all0.4125 1241 -
obs--36.9 %
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)
12.27150.4631-1.16793.3983-0.80652.6272-0.0439-0.1681-0.452-0.54420.01630.54330.0642-0.01040.02760.00640.08420.0577-0.2025-0.01720.0046-25.0914-10.9172-18.4023
22.840.40040.28968.31541.16151.39330.00670.2573-0.0539-0.43180.0235-0.03910.01590.0273-0.03010.08990.04080.0159-0.2195-0.0039-0.1701-20.11066.516-28.305
34.1843-0.11441.85842.6863-0.11723.6448-0.03710.34920.2113-0.5442-0.00120.2681-0.20830.06130.0383-0.00820.08090.02-0.1928-0.0021-0.1071-20.78167.2229-28.3881
42.7286-0.3056-0.75383.166-0.40182.08-0.2954-0.54420.21760.54420.24880.3683-0.1561-0.26450.0466-0.08790.11270.13070.0559-0.0449-0.1475-24.14095.7348-3.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|161 - A|198 }A161 - 198
2X-RAY DIFFRACTION2{ A|199 - A|253 }A199 - 253
3X-RAY DIFFRACTION3{ A|254 - A|388 }A254 - 388
4X-RAY DIFFRACTION4{ A|389 - A|520 }A389 - 520

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