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- PDB-4o67: Human cyclic GMP-AMP synthase (cGAS) in complex with GAMP -

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Basic information

Entry
Database: PDB / ID: 4o67
TitleHuman cyclic GMP-AMP synthase (cGAS) in complex with GAMP
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / immune response
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
cGAMP / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.444 Å
AuthorsZhang, X. / Chen, Z. / Zhang, X.W. / Chen, Z.J.
CitationJournal: Cell Rep / Year: 2014
Title: The Cytosolic DNA Sensor cGAS Forms an Oligomeric Complex with DNA and Undergoes Switch-like Conformational Changes in the Activation Loop.
Authors: Zhang, X. / Wu, J. / Du, F. / Xu, H. / Sun, L. / Chen, Z. / Brautigam, C.A. / Zhang, X. / Chen, Z.J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Aug 5, 2015Group: Non-polymer description
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5526
Polymers85,0722
Non-polymers1,4804
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2763
Polymers42,5361
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Cyclic GMP-AMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2763
Polymers42,5361
Non-polymers7402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.822, 118.542, 124.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclic GMP-AMP synthase


Mass: 42536.102 Da / Num. of mol.: 2 / Fragment: UNP residues 161-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N884
#2: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2% Isopropanol, 0.01 M MgSO4, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 26922 / Num. obs: 26688 / % possible obs: 99.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.44→2.48 Å / % possible all: 92.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.444→37.869 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2806 1327 4.99 %
Rwork0.2004 --
obs0.2044 26593 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.444→37.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5703 0 92 89 5884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015915
X-RAY DIFFRACTIONf_angle_d1.2997944
X-RAY DIFFRACTIONf_dihedral_angle_d15.2022282
X-RAY DIFFRACTIONf_chiral_restr0.056867
X-RAY DIFFRACTIONf_plane_restr0.006984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4437-2.54160.39411340.30362586X-RAY DIFFRACTION92
2.5416-2.65720.39511330.2782818X-RAY DIFFRACTION99
2.6572-2.79730.34891540.24912751X-RAY DIFFRACTION100
2.7973-2.97250.33151470.23642808X-RAY DIFFRACTION100
2.9725-3.20190.32161490.23512816X-RAY DIFFRACTION100
3.2019-3.52390.27591520.20652798X-RAY DIFFRACTION100
3.5239-4.03330.22591450.17962866X-RAY DIFFRACTION100
4.0333-5.07960.26681520.15692862X-RAY DIFFRACTION100
5.0796-37.87390.23871610.18072961X-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)
10.0399-0.4262-0.27610.0231-0.02540.13160.1018-0.2134-0.01140.2247-0.230.38130.1359-0.061-00.29870.03080.01410.32940.04840.3639-1.734744.4271147.6493
20.1930.29560.08930.62160.16590.274-0.0623-0.053-0.137-0.11410.1609-0.09590.01080.0582-00.41330.00830.0280.284-0.06790.396616.899728.1716137.4425
30.33260.1164-0.08420.78830.42630.3911-0.044-0.02050.0001-0.03630.03540.06150.02790.0469-00.19770.00050.00380.1777-0.02520.175112.173539.0332141.2603
40.77770.22680.12370.32280.04680.6896-0.05080.12470.1476-0.04370.08520.0071-0.02620.040200.1736-0.0051-0.00120.15110.00830.17258.914157.4441133.0457
50.4544-0.16860.28780.03780.02930.35090.0430.02090.0430.4422-0.2220.19550.10460.011300.22630.0440.10260.30790.06190.3323-1.3981103.4912147.5072
60.41140.4764-0.03490.6441-0.08450.16520.16250.1785-0.15290.1565-0.0606-0.02290.03380.1637-00.43490.08950.04850.3734-0.05960.39515.314690.6318138.2808
70.70880.1091-0.06631.28050.3131-0.292-0.07510.2294-0.00270.0604-0.02460.14790.02910.175700.2367-0.00860.04030.2293-0.00490.201613.467194.7896140.398
80.9797-0.2087-0.3689-0.02420.18270.7868-0.05040.1264-0.0295-0.07060.0261-0.0267-0.1037-0.0292-00.2299-0.0041-0.02340.22530.07140.18269.0418115.606131.8826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 199 )
2X-RAY DIFFRACTION2chain 'A' and (resid 200 through 272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 405 )
4X-RAY DIFFRACTION4chain 'A' and (resid 406 through 521 )
5X-RAY DIFFRACTION5chain 'B' and (resid 161 through 199 )
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 253 )
7X-RAY DIFFRACTION7chain 'B' and (resid 254 through 405 )
8X-RAY DIFFRACTION8chain 'B' and (resid 406 through 521 )

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