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- PDB-4lew: Structure of human cGAS -

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Basic information

Entry
Database: PDB / ID: 4lew
TitleStructure of human cGAS
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / NTase / DNA sensor
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 / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway ...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 / regulation of immunoglobulin production / cGAS/STING signaling pathway / pattern recognition receptor signaling pathway / regulation of T cell activation / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / 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 / cAMP-mediated signaling / 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 / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
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: 2.04 Å
AuthorsLi, P.
CitationJournal: Immunity / Year: 2013
Title: Cyclic GMP-AMP Synthase Is Activated by Double-Stranded DNA-Induced Oligomerization.
Authors: Li, X. / Shu, C. / Yi, G. / Chaton, C.T. / Shelton, C.L. / Diao, J. / Zuo, X. / Kao, C.C. / Herr, A.B. / Li, P.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cyclic GMP-AMP synthase
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1184
Polymers85,9872
Non-polymers1312
Water6,539363
1
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0592
Polymers42,9941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0592
Polymers42,9941
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.815, 111.480, 76.414
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42993.742 Da / Num. of mol.: 2 / Fragment: Catalytic domain, 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% PEG 3350, 0.2 M A.S., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.04→43.1 Å / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 31.2
Reflection shellResolution: 2.04→2.08 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.04→40.747 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3973 4.06 %Random
Rwork0.1787 ---
obs0.1805 97840 99.57 %-
all-98377 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→40.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 2 363 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096030
X-RAY DIFFRACTIONf_angle_d1.1228089
X-RAY DIFFRACTIONf_dihedral_angle_d14.8092331
X-RAY DIFFRACTIONf_chiral_restr0.078876
X-RAY DIFFRACTIONf_plane_restr0.0061029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0398-2.06470.28741400.26073159X-RAY DIFFRACTION95
2.0647-2.09080.28791580.24253346X-RAY DIFFRACTION100
2.0908-2.11830.29951250.22873428X-RAY DIFFRACTION100
2.1183-2.14730.23471400.22453297X-RAY DIFFRACTION100
2.1473-2.1780.24291600.21363358X-RAY DIFFRACTION100
2.178-2.21050.27091350.2083384X-RAY DIFFRACTION100
2.2105-2.2450.20621430.19713371X-RAY DIFFRACTION100
2.245-2.28180.25181480.19763332X-RAY DIFFRACTION100
2.2818-2.32120.21721260.1893417X-RAY DIFFRACTION100
2.3212-2.36340.24921590.18253342X-RAY DIFFRACTION100
2.3634-2.40880.26341260.19053325X-RAY DIFFRACTION100
2.4088-2.4580.22361540.18343413X-RAY DIFFRACTION100
2.458-2.51140.23631260.17383312X-RAY DIFFRACTION100
2.5114-2.56990.17741470.16743396X-RAY DIFFRACTION100
2.5699-2.63410.25291430.18433366X-RAY DIFFRACTION100
2.6341-2.70530.2131500.17593328X-RAY DIFFRACTION100
2.7053-2.78490.22661190.18183394X-RAY DIFFRACTION100
2.7849-2.87480.2841520.19873358X-RAY DIFFRACTION100
2.8748-2.97750.31111420.1933329X-RAY DIFFRACTION100
2.9775-3.09670.24231350.19633437X-RAY DIFFRACTION100
3.0967-3.23750.25511430.18743316X-RAY DIFFRACTION100
3.2375-3.40820.2111510.17463377X-RAY DIFFRACTION100
3.4082-3.62160.20961320.16553402X-RAY DIFFRACTION100
3.6216-3.9010.20331440.16213346X-RAY DIFFRACTION100
3.901-4.29320.19441380.15063364X-RAY DIFFRACTION99
4.2932-4.91350.1751510.14943322X-RAY DIFFRACTION100
4.9135-6.1870.191450.17373345X-RAY DIFFRACTION99
6.187-40.75520.23091410.17943303X-RAY DIFFRACTION98
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)
1-0.33491.6196-0.684.2775-1.33910.27250.05150.36790.3033-0.16880.20011.09870.0079-0.5895-0.13270.5272-0.09460.00950.62440.16150.8515-22.168378.267762.044
22.2824-1.71730.97173.0337-1.11993.09730.0076-0.24670.49860.65380.2304-0.4263-1.0320.3256-0.26240.8-0.16430.11790.4165-0.0910.4472-5.841495.096369.8216
31.6426-0.1797-0.49822.40840.57712.83710.0709-0.29010.34710.24320.1090.2722-0.4152-0.0432-0.13380.2411-0.04940.06970.3303-0.0190.2583-10.07580.085366.8447
41.2869-0.2065-1.22681.750.83574.0756-0.1723-0.1474-0.07210.46770.00870.19040.5935-0.17090.10030.3381-0.03830.0290.34180.06230.194-12.928864.787577.9333
52.55661.22260.05658.15251.22972.99310.3084-0.1272-0.37830.3818-0.0344-0.62560.02350.3017-0.15870.25130.0109-0.03060.24980.07720.404122.669856.228341.2551
61.93991.79020.84793.02031.02331.60070.0692-0.04720.0178-0.15430.0027-0.4532-0.1820.0090.00050.19190.00440.00980.1761-0.02150.38227.773386.172733.5728
71.30810.3895-0.45643.1624-0.19250.9591-0.0935-0.01170.1758-0.31810.188-0.51-0.09220.0606-0.1030.1523-0.01080.03630.1901-0.05530.25178.536777.283535.0272
82.1401-0.4061-0.35791.70680.27893.00360.03890.1727-0.197-0.4038-0.1146-0.1080.18560.14770.03550.23870.03830.02120.0986-0.00350.173510.028257.491129.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 162 through 224 )
2X-RAY DIFFRACTION2chain 'B' and (resid 225 through 286 )
3X-RAY DIFFRACTION3chain 'B' and (resid 287 through 405 )
4X-RAY DIFFRACTION4chain 'B' and (resid 406 through 520 )
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 405 )
8X-RAY DIFFRACTION8chain 'A' and (resid 406 through 520 )

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