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- PDB-8si0: Structure of binary complex of human cGAS and bound cGAMP -

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Basic information

Entry
Database: PDB / ID: 8si0
TitleStructure of binary complex of human cGAS and bound cGAMP
ComponentsCyclic GMP-AMP synthase
KeywordsTRANSFERASE / IMMUNE SYSTEM
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 / cytoplasm / cytosol
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
cGAMP / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, S. / Sohn, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2024
Title: The structural basis for 2'-5'/3'-5'-cGAMP synthesis by cGAS.
Authors: Wu, S. / Gabelli, S.B. / Sohn, J.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)43,7143
Polymers42,9741
Non-polymers7402
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.927, 59.657, 125.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 42974.473 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 157-522)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGAS, C6orf150, MB21D1 / Plasmid: nHMT hCAT WT
Details (production host): His*6-MBP-Tev-AgeI-hcGAS CAT, Kanamycin resistance
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N884, cyclic GMP-AMP synthase
#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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5 mM magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 8% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationMonochromator: horizontal bounce Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→27.85 Å / Num. obs: 10385 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.032 / Rrim(I) all: 0.072 / Χ2: 1 / Net I/σ(I): 15.3 / Num. measured all: 47898
Reflection shellResolution: 2.7→2.83 Å / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.161 / Num. measured all: 6487 / Num. unique obs: 1374 / CC1/2: 0.984 / Rpim(I) all: 0.083 / Rrim(I) all: 0.182 / Χ2: 0.94 / Net I/σ(I) obs: 7.3

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
Coot0.9.6model building
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4O67

4o67


Resolution: 2.7→27.85 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 1023 10 %
Rwork0.2169 --
obs0.2231 10230 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 46 2 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.121
X-RAY DIFFRACTIONf_dihedral_angle_d12.599384
X-RAY DIFFRACTIONf_chiral_restr0.056440
X-RAY DIFFRACTIONf_plane_restr0.009503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.840.38091450.30941310X-RAY DIFFRACTION99
2.84-3.020.30931410.26791268X-RAY DIFFRACTION99
3.02-3.250.33851390.26441252X-RAY DIFFRACTION96
3.25-3.580.31281470.24291320X-RAY DIFFRACTION99
3.58-4.10.27581470.20631322X-RAY DIFFRACTION100
4.1-5.150.23111480.18271335X-RAY DIFFRACTION99
5.16-27.850.25381560.18421400X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.4772 Å / Origin y: -14.1336 Å / Origin z: -16.7636 Å
111213212223313233
T0.258 Å2-0.1024 Å2-0.0307 Å2-0.2217 Å20.043 Å2--0.0212 Å2
L2.5319 °2-0.4494 °20.4245 °2-0.3826 °2-0.2435 °2--0.9469 °2
S-0.3516 Å °1.3151 Å °-0.1774 Å °0.0382 Å °0.0071 Å °-0.133 Å °-0.2966 Å °0.237 Å °-0.3933 Å °
Refinement TLS groupSelection details: (chain A and resseq 161:521) or (chain A and resseq 602:602)

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