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- PDB-6ct9: Structure of the human cGAS-DNA complex -

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Basic information

Entry
Database: PDB / ID: 6ct9
TitleStructure of the human cGAS-DNA complex
Components
  • Cyclic GMP-AMP synthase
  • DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*A)-3')
  • DNA (5'-D(P*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)-3')
KeywordsTRANSFERASE/DNA / cGAS / STING / Innate Immunity / transferase / TRANSFERASE-DNA complex
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
DNA / DNA (> 10) / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsZhou, W. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Mekalanos, J.J. / Kranzusch, P.J.
CitationJournal: Cell / Year: 2018
Title: Structure of the Human cGAS-DNA Complex Reveals Enhanced Control of Immune Surveillance.
Authors: Zhou, W. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Nowak, R.P. / Fischer, E.S. / Gray, N.S. / Mekalanos, J.J. / Kranzusch, P.J.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic GMP-AMP synthase
B: DNA (5'-D(P*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)-3')
C: DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3544
Polymers53,2883
Non-polymers651
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-19 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.782, 99.782, 236.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 42875.305 Da / Num. of mol.: 1 / Mutation: K187N, L195R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#2: DNA chain DNA (5'-D(P*CP*GP*TP*CP*TP*TP*CP*GP*GP*CP*AP*AP*T)-3')


Mass: 5159.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*TP*TP*GP*CP*CP*GP*AP*AP*GP*AP*CP*GP*A)-3')


Mass: 5253.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES-NaOH pH 7.0, 1.4 M sodium citrate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→48.21 Å / Num. obs: 33460 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rpim(I) all: 0.045 / Net I/av σ(I): 10.9 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.317 / Rpim(I) all: 0.796 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KM5

4km5


Resolution: 2.26→45.975 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 3316 10 %
Rwork0.1993 --
obs0.2021 33166 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→45.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 592 1 103 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063577
X-RAY DIFFRACTIONf_angle_d0.724924
X-RAY DIFFRACTIONf_dihedral_angle_d19.1112069
X-RAY DIFFRACTIONf_chiral_restr0.042539
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2599-2.29220.398990.3338892X-RAY DIFFRACTION73
2.2922-2.32640.3611380.31771240X-RAY DIFFRACTION100
2.3264-2.36270.32281360.30641214X-RAY DIFFRACTION100
2.3627-2.40150.34241370.3071244X-RAY DIFFRACTION100
2.4015-2.44290.3411340.28781220X-RAY DIFFRACTION100
2.4429-2.48730.3181360.27851222X-RAY DIFFRACTION100
2.4873-2.53510.32381380.26641236X-RAY DIFFRACTION100
2.5351-2.58690.34331360.26981230X-RAY DIFFRACTION100
2.5869-2.64310.27651390.26241248X-RAY DIFFRACTION100
2.6431-2.70460.33011390.25051242X-RAY DIFFRACTION100
2.7046-2.77220.32011360.25221230X-RAY DIFFRACTION100
2.7722-2.84720.25131370.24941241X-RAY DIFFRACTION100
2.8472-2.93090.27981400.2361250X-RAY DIFFRACTION100
2.9309-3.02550.24951380.22171232X-RAY DIFFRACTION100
3.0255-3.13360.24241390.22141255X-RAY DIFFRACTION100
3.1336-3.25910.25021390.19821249X-RAY DIFFRACTION100
3.2591-3.40730.2381380.19961253X-RAY DIFFRACTION100
3.4073-3.58690.22721400.18251262X-RAY DIFFRACTION100
3.5869-3.81150.20231410.17491270X-RAY DIFFRACTION100
3.8115-4.10570.18751420.15731267X-RAY DIFFRACTION100
4.1057-4.51850.16161420.15391288X-RAY DIFFRACTION100
4.5185-5.17160.18581440.14441298X-RAY DIFFRACTION100
5.1716-6.51270.21131480.18561327X-RAY DIFFRACTION100
6.5127-45.98460.20131600.19711440X-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)
10.0796-0.1763-0.04920.32540.1040.01750.08250.25970.6902-0.1413-0.1250.4104-0.6142-0.0239-0.00080.68010.0170.03760.41360.06680.558434.9195-19.5055-1.8017
20.3566-0.3601-0.33050.32270.29470.19980.08280.48710.59690.55780.23920.4848-0.1942-0.1342-00.4760.01610.00080.55480.05610.61519.0951-32.8619-0.0439
30.05-0.0126-0.03090.0227-0.05550.1124-0.55240.2936-0.18360.5389-0.1414-0.2043-0.0877-0.10720.00230.53570.04080.05570.94060.08450.84074.5542-52.04931.6124
40.18170.360.17470.1939-0.02040.1088-0.1160.5560.0686-0.15370.0856-0.37960.05480.103-0.00020.5782-0.0195-0.02670.75090.03250.679420.0855-35.6671-0.0268
50.237-0.2220.11060.2505-0.11640.02540.5021-0.241-0.46780.0407-0.001-0.09470.46190.3763-0.00150.6116-0.0358-0.06160.6275-0.06190.731724.433-60.2691-0.4776
6-0.0050.0575-0.00880.30820.0095-0.0283-0.63050.1628-0.44560.24760.58990.36970.5201-0.1134-0.00130.5617-0.00990.05340.5255-0.06710.72613.479-61.6379-0.0379
70.0609-0.03520.01930.09850.04430.0392-0.21440.3571-0.4204-0.12870.04160.52170.4645-0.34750.00050.6329-0.14950.10550.7899-0.27440.936513.6932-64.0301-5.6698
80.23770.23350.03240.2037-0.07560.2501-0.08270.5435-0.2552-0.86040.00740.53470.1069-0.3787-0.00120.5297-0.0221-0.04630.8553-0.08150.52587.1527-47.6403-9.402
90.6859-0.9463-0.90014.35643.93853.59370.06880.03070.2351-0.28971.01720.3692-0.4778-0.53220.56290.80470.1505-0.15351.05690.29960.77736.5329-34.9924-12.0591
100.42510.13630.0590.04240.04610.01990.02320.30520.0044-0.0689-0.0779-0.187-0.02020.0216-00.39240.01730.02590.55550.03090.478818.8067-43.9713-3.0492
110.69920.4947-0.65450.1717-0.31540.57140.00580.1222-0.37140.0836-0.0499-0.12750.2894-0.00130.00010.34480.01760.01080.37240.01560.378332.2402-48.437910.511
12-0.03370.12830.0150.2546-0.0691-0.0065-0.22610.19430.1749-0.3386-0.14880.4661-0.2305-0.1014-0.00020.3477-0.0183-0.00570.5716-0.01750.48125.2161-49.2562-2.9364
130.02450.0812-0.06970.5978-0.14880.31460.08450.11720.1079-0.05770.06520.0988-0.3218-0.031-0.00020.39680.0073-0.02640.47040.04450.408935.0959-30.8529-2.2999
140.1501-0.1695-0.2071.117-0.94031.05430.0230.08290.0009-0.09640.0814-0.1130.04790.16420.00010.3467-0.00230.01140.46940.00440.402540.9076-39.6016-1.621
150.1316-0.19780.20190.3179-0.37550.37260.12480.16560.0378-0.497-0.024-0.3885-0.39150.28190.00040.48310.04560.06640.57050.06480.335843.3826-30.6751-14.887
160.3281-0.4020.01570.4625-0.17391.16540.1608-1.73350.6796-0.1927-0.69970.1641-0.3277-0.6001-0.02621.0144-0.2665-0.05011.3478-0.09681.127215.7612-28.635715.516
170.6359-0.27480.15920.51010.7491.190.4036-0.80940.7905-0.2563-0.74160.8441-0.44810.0573-0.00021.1752-0.1694-0.12920.95110.04231.23514.9188-29.568713.4958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 175 )
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 205 )
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 232 )
5X-RAY DIFFRACTION5chain 'A' and (resid 233 through 248 )
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 272 )
8X-RAY DIFFRACTION8chain 'A' and (resid 273 through 289 )
9X-RAY DIFFRACTION9chain 'A' and (resid 290 through 299 )
10X-RAY DIFFRACTION10chain 'A' and (resid 303 through 334 )
11X-RAY DIFFRACTION11chain 'A' and (resid 335 through 361 )
12X-RAY DIFFRACTION12chain 'A' and (resid 362 through 388 )
13X-RAY DIFFRACTION13chain 'A' and (resid 389 through 434 )
14X-RAY DIFFRACTION14chain 'A' and (resid 435 through 497 )
15X-RAY DIFFRACTION15chain 'A' and (resid 498 through 521 )
16X-RAY DIFFRACTION16chain 'B' and (resid 4 through 16 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 16 )

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