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- PDB-7fu3: Crystal Structure of human cyclic GMP-AMP synthase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7fu3
TitleCrystal Structure of human cyclic GMP-AMP synthase in complex with 8-chloro-2-(2-hydroxyphenyl)quinoline-4-carboxylic acid
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE RESPONSE / NTASE / DNA SENSOR
Function / homology
Function and homology information


water channel activity / plasma membrane
Similarity search - Function
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
: / Probable aquaporin AqpM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.822 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

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7703
Polymers42,4051
Non-polymers3652
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)47.798, 58.695, 124.929
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-YME / (2P)-8-chloro-2-(2-hydroxyphenyl)quinoline-4-carboxylic acid


Mass: 299.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10ClNO3 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
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: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.82→58.7 Å / Num. obs: 32267 / % possible obs: 99.9 % / Redundancy: 6.447 % / Biso Wilson estimate: 50.347 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.093 / Χ2: 0.789 / Net I/σ(I): 10.99 / Num. measured all: 208031 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.82-1.876.0666.9560.2314201234323417.61699.9
1.87-1.926.7085.1470.3415388229622945.57799.90.148
1.92-1.986.7823.5780.5215070222622223.87499.80.236
1.98-2.046.6882.320.8314366214821482.5161000.385
2.04-2.16.5791.7051.1213921211621161.8521000.51
2.1-2.186.4131.1981.6213108204520441.3041000.716
2.18-2.266.0750.8762.1411859195219520.961000.761
2.26-2.356.7520.5963.3412862190519050.6461000.917
2.35-2.466.750.4724.0612231181218120.5111000.935
2.46-2.586.7270.3175.8411664173517340.34499.90.965
2.58-2.726.5550.2337.6310940166916690.2531000.98
2.72-2.886.120.15910.549706158615860.1741000.99
2.88-3.086.5870.11215.559723147614760.1221000.995
3.08-3.336.7060.07721.749388140214000.08499.90.997
3.33-3.646.4960.0531.98445130013000.0551000.999
3.64-4.075.880.0437.616868117011680.04499.80.999
4.07-4.76.0150.0346.046280104410440.0331000.999
4.7-5.766.3220.02848.1957159059040.03199.90.999
5.76-8.155.5340.02845.8539577167150.03199.90.999
8.15-58.6955.3520.01955.0423394424370.02198.91

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.822→58.695 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 1036 4.88 %RANDOM
Rwork0.1937 20192 --
obs0.1971 21228 65.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.51 Å2 / Biso mean: 58.5103 Å2 / Biso min: 12.65 Å2
Refinement stepCycle: final / Resolution: 1.822→58.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 22 73 2962
Biso mean--55.36 41.51 -
Num. residues----349
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 (%)
1.8224-1.91850.446580.32751841924
1.9185-2.03870.2842260.273155257813
2.0387-2.19610.3125980.25992106220449
2.1961-2.41710.28282130.2543974418792
2.4171-2.76680.29632220.237743744596100
2.7668-3.48590.26792190.209544134632100
3.4859-58.72540.2462500.157345894839100
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)
11.7258-1.98890.43842.50840.06991.5594-0.1495-0.01880.29270.66320.1423-1.0316-0.33750.09430.01790.36360.0766-0.01070.37820.00160.382825.4613-13.9791-7.3669
23.4181.9440.70283.76690.77683.5343-0.11540.24520.4422-0.09220.0154-0.0035-0.71030.1630.0880.75910.0764-0.08870.38140.1420.511811.69392.1614-17.3798
32.0325-0.09630.1242.5341-0.27752.0631-0.06390.38990.4717-0.2852-0.0372-0.2145-0.4880.1969-0.01890.2672-0.022-0.01830.24610.08510.306410.3349-10.7685-13.4598
43.0338-0.5672-0.42512.5362-0.20882.8897-0.00120.4796-0.1857-0.5479-0.1166-0.05210.21460.20010.11370.22570.0149-0.00780.2057-0.04760.140614.7856-26.8297-22.675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 199 )A161 - 199
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 290 )A200 - 290
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 405 )A291 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 521 )A406 - 521

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