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- PDB-7buq: mcGAS bound with 23-cGAMP -

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Basic information

Entry
Database: PDB / ID: 7buq
TitlemcGAS bound with 23-cGAMP
ComponentsCyclic GMP-AMP synthase
KeywordsIMMUNE SYSTEM / mcGAS / activator / inverted-orientation / metal-ion binding protein
Function / homology
Function and homology information


regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / cGAS/STING signaling pathway / regulation of immunoglobulin production / regulation of T cell activation / pattern recognition receptor signaling pathway ...regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / 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 / regulation of immune response / 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
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
Similarity search - Domain/homology
cGAMP / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.091 Å
AuthorsWang, B. / Su, X.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31670740 China
National Science Foundation (NSF, China)31270803 China
CitationJournal: Cell Rep / Year: 2020
Title: Mn2+Directly Activates cGAS and Structural Analysis Suggests Mn2+Induces a Noncanonical Catalytic Synthesis of 2'3'-cGAMP.
Authors: Zhao, Z. / Ma, Z. / Wang, B. / Guan, Y. / Su, X.D. / Jiang, Z.
History
DepositionApr 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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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)118,0796
Polymers116,6002
Non-polymers1,4804
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.645, 109.812, 75.637
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 58299.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cgas, Mb21d1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C6L5, cyclic GMP-AMP synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1SY / cGAMP / 2',3' cGAMP / c-GMP-AMP / c[G(2',5')pA(3',5')p] / Cyclic guanosine monophosphate–adenosine monophosphate


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.69 Å3/Da / Density % sol: 27.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-Tris, 25 % w/v PEG-3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.091→50 Å / Num. obs: 14136 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.104 / Rrim(I) all: 0.271 / Χ2: 0.984 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.155.41.0487290.60.4821.1570.97599.7
3.15-3.215.70.8856760.6890.3970.9720.96499.6
3.21-3.275.50.7956920.70.3670.8791.02698.2
3.27-3.346.30.7287020.7790.3130.7950.99497.1
3.34-3.4170.6767060.8390.2740.7310.978100
3.41-3.496.90.6026810.8850.2470.6521.123100
3.49-3.5870.4867120.9120.1970.5251.047100
3.58-3.687.10.4377180.9440.1780.4731.121100
3.68-3.7870.3856930.9340.1560.4150.99599.9
3.78-3.916.90.347120.9490.1380.3681.14899.9
3.91-4.046.90.2916930.9630.1180.3141.02699.7
4.04-4.216.60.2317060.9760.0970.2510.98399.7
4.21-4.46.20.1857100.9790.080.2020.9999.4
4.4-4.637.30.1737050.9840.0690.1860.93399.9
4.63-4.927.20.1547030.9850.0620.1660.90999.9
4.92-5.37.10.147230.9910.0560.1510.832100
5.3-5.836.90.1627170.9850.0660.1760.862100
5.83-6.676.20.1497170.9810.0650.1630.81899.9
6.67-8.47.20.1117140.9930.0440.120.822100
8.4-506.40.0997270.9830.0420.1081.16299

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.69 Å44.39 Å
Translation6.69 Å44.39 Å

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000V715data reduction
SCALEPACKdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K96

4k96


Resolution: 3.091→37.72 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2963 1402 10.1 %
Rwork0.2493 --
obs0.254 13881 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.55 Å2 / Biso mean: 67.1826 Å2 / Biso min: 25.4 Å2
Refinement stepCycle: final / Resolution: 3.091→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 92 1 6070
Biso mean--129.1 52.41 -
Num. residues----723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.091-3.20090.38451240.3367104282
3.2009-3.3290.34431360.3053119293
3.329-3.48040.3621220.2804127099
3.4804-3.66380.29331580.26421281100
3.6638-3.89310.3021400.25841266100
3.8931-4.19330.35071430.24221281100
4.1933-4.61460.26731390.22441280100
4.6146-5.28080.25841420.22841292100
5.2808-6.64740.31431480.26561286100
6.6474-37.720.25181500.2218128999
Refinement TLS params.Method: refined / Origin x: 9.1561 Å / Origin y: 1.2781 Å / Origin z: -16.5842 Å
111213212223313233
T0.3131 Å2-0.0194 Å20.0272 Å2-0.3088 Å2-0.014 Å2--0.3109 Å2
L0.3395 °2-0.1014 °20.134 °2-0.366 °2-0.0901 °2--0.3942 °2
S-0.0127 Å °-0.0445 Å °0.054 Å °0.0358 Å °-0.0053 Å °-0.0284 Å °0.0222 Å °-0.0213 Å °0.0238 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA146 - 507
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allA701
4X-RAY DIFFRACTION1allB147 - 507
5X-RAY DIFFRACTION1allB601
6X-RAY DIFFRACTION1allB701
7X-RAY DIFFRACTION1allC2

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