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- PDB-7bum: mcGAS bound with pGpA -

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Basic information

Entry
Database: PDB / ID: 7bum
TitlemcGAS bound with pGpA
ComponentsCyclic GMP-AMP synthase
KeywordsIMMUNE SYSTEM / cGAS / 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 cGAS/STING signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / cGMP-mediated signaling / positive regulation of type I interferon production / regulation of immune response / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / cAMP-mediated signaling / 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
GUANOSINE-5'-MONOPHOSPHATE / ADENOSINE MONOPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.047 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
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_site.pdbx_auth_comp_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)118,1518
Polymers116,6002
Non-polymers1,5526
Water66737
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)48.337, 109.592, 75.870
Angle α, β, γ (deg.)90.000, 93.930, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.72 Å3/Da / Density % sol: 28.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES, 30 % w/v PEG-5000 MME, 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: 3.047→50 Å / Num. obs: 15010 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.085 / Rrim(I) all: 0.21 / Χ2: 0.981 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.14.10.867180.5790.4650.9830.9198.5
3.1-3.164.30.8097320.6420.4310.9210.91298.8
3.16-3.224.30.7087620.6640.3750.8060.93898.6
3.22-3.294.40.5887170.7270.3110.6680.92597.6
3.29-3.3650.6027400.7930.2940.6720.92899.7
3.36-3.435.60.547810.8430.250.5970.97100
3.43-3.525.60.4797330.8840.2210.5280.968100
3.52-3.625.90.3967570.9230.1770.4350.979100
3.62-3.726.10.3937600.9170.1740.4311.01699.7
3.72-3.846.20.3157380.9620.1380.3450.963100
3.84-3.986.20.2777580.9610.120.3020.95599.6
3.98-4.146.20.2297490.9730.1010.2511.01999.5
4.14-4.335.70.1757310.980.080.1930.99498.5
4.33-4.566.50.1627650.9860.0690.1771.005100
4.56-4.846.80.1437570.9920.0590.1550.995100
4.84-5.216.90.1437590.9930.0580.1541.055100
5.21-5.746.90.1617550.990.0660.1740.98999.7
5.74-6.576.10.1527490.9840.0670.1670.92499.2
6.57-8.277.10.117690.9950.0440.1180.96100
8.27-506.50.077800.9960.030.0761.09299.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.77 Å44.14 Å
Translation6.77 Å44.14 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: 3.047→30.816 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.2
RfactorNum. reflection% reflection
Rfree0.2801 1449 10.05 %
Rwork0.2167 --
obs0.2232 14412 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.83 Å2 / Biso mean: 68.2371 Å2 / Biso min: 25.47 Å2
Refinement stepCycle: final / Resolution: 3.047→30.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 94 37 6099
Biso mean--99.61 57.32 -
Num. residues----722
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0472-3.1560.39441030.306895872
3.156-3.28230.33651210.2702117386
3.2823-3.43140.3591440.2668135998
3.4314-3.61210.31681470.24361335100
3.6121-3.8380.30731630.22581342100
3.838-4.13370.26121450.211135399
4.1337-4.54850.24591550.1883134599
4.5485-5.2040.24771520.18681369100
5.204-6.54610.33471540.2286134599
6.5461-30.810.22921650.1954138499
Refinement TLS params.Method: refined / Origin x: 8.7547 Å / Origin y: 1.2011 Å / Origin z: -16.8497 Å
111213212223313233
T0.2796 Å2-0.0293 Å20.0347 Å2-0.2975 Å2-0.0313 Å2--0.3324 Å2
L0.5412 °2-0.2197 °20.2635 °2-0.3537 °2-0.2329 °2--0.5298 °2
S-0.0159 Å °-0.0574 Å °0.0799 Å °0.0173 Å °0.0259 Å °-0.0132 Å °-0.0135 Å °-0.0307 Å °0.0106 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA147 - 801
2X-RAY DIFFRACTION1allB147 - 801
3X-RAY DIFFRACTION1allW1 - 43

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