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- PDB-4jlz: Structure of porcine cGAS in complex with bound UTP -

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Basic information

Entry
Database: PDB / ID: 4jlz
TitleStructure of porcine cGAS in complex with bound UTP
ComponentsUncharacterized protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / 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 ...cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / 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 / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / 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
URIDINE 5'-TRIPHOSPHATE / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsCivril, F. / Hopfner, K.P.
CitationJournal: Nature / Year: 2013
Title: Structural mechanism of cytosolic DNA sensing by cGAS
Authors: Civril, F. / Deimling, T. / Mann, C.C.O. / Ablasser, A. / Moldt, M. / Witte, G. / Hornung, V. / Hopfner, K.P.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0928
Polymers84,9442
Non-polymers1,1486
Water4,954275
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0464
Polymers42,4721
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0464
Polymers42,4721
Non-polymers5743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.560, 97.693, 106.959
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 Uncharacterized protein


Mass: 42472.164 Da / Num. of mol.: 2 / Fragment: UNP residues 135-495
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: MB21D1 / Production host: Escherichia coli (E. coli) / References: UniProt: I3LM39
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICTS (ASP 268 AND THR 269) ARE DUE TO POLYMORPHISM AS IT IS NATURALLY OCCURRING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.35 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.27→46.9 Å / Num. obs: 72224

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→44.556 Å / SU ML: 0.27 / σ(F): 1.18 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 3594 4.98 %
Rwork0.1719 --
obs0.1736 72224 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→44.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 62 275 6215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116173
X-RAY DIFFRACTIONf_angle_d1.2398329
X-RAY DIFFRACTIONf_dihedral_angle_d15.4892370
X-RAY DIFFRACTIONf_chiral_restr0.079887
X-RAY DIFFRACTIONf_plane_restr0.0061053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.27-2.29960.30611120.2935219480
2.2996-2.33110.31241370.263266697
2.3311-2.36440.30941410.2492265298
2.3644-2.39970.28511410.2388267897
2.3997-2.43720.28571440.2334275698
2.4372-2.47710.28841420.23269098
2.4771-2.51980.31341370.2283267098
2.5198-2.56560.28041340.2138269498
2.5656-2.6150.23061460.2088272298
2.615-2.66840.24861370.2046264196
2.6684-2.72640.22051420.1922265296
2.7264-2.78980.26741410.1951266696
2.7898-2.85950.19361410.1806267697
2.8595-2.93680.23021410.1876267898
2.9368-3.02320.21231380.1806271298
3.0232-3.12080.22361440.1767272298
3.1208-3.23230.20821410.1721269697
3.2323-3.36170.22921420.1613266197
3.3617-3.51460.19071330.1663263195
3.5146-3.69980.20461340.1615250792
3.6998-3.93150.15921350.1456259794
3.9315-4.23490.19741390.1437261595
4.2349-4.66060.16721360.1302260295
4.6606-5.33410.15721370.1322259494
5.3341-6.71660.17491360.1835263095
6.7166-44.56410.19671430.1678262896
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)
11.5867-0.2687-0.20262.0144-0.93152.7172-0.00840.47840.2135-0.1305-0.1016-0.323-0.11370.12680.10320.2028-0.0162-0.0040.26430.04720.2623-22.0812-10.938-1.2014
28.033-0.7199-1.93242.2476-0.47152.21630.00960.32410.9767-0.1386-0.1352-0.339-0.38190.15940.08610.2622-0.076-0.00570.32520.10810.3108-28.4169-0.2387-4.4688
32.88931.337-1.38694.7156-2.34672.8135-0.1030.38880.30380.01030.0171-0.2596-0.1138-0.10790.11670.10370.0047-0.01080.18820.03460.2257-13.8321-19.66445.236
43.2884-0.8136-1.19362.11731.39292.788-0.013-0.28920.41140.23820.0642-0.2597-0.20090.1703-0.04450.1874-0.0051-0.06740.1509-0.01820.1748-21.4355-15.878823.0256
51.9450.268-0.31874.5887-2.48614.4461-0.04260.0618-0.0059-0.07720.1234-0.08250.09630.1195-0.00110.20770.0478-0.04720.1805-0.07250.1878-45.5093-2.474317.2059
62.63690.18941.66611.56560.36373.642-0.071-0.5825-0.02440.4350.03330.30290.004-0.66310.02060.27190.04780.0320.2723-0.00980.2716-61.5835-6.045624.386
71.09250.0593-0.45573.14011.17072.19160.08740.0610.1697-0.263-0.1790.2636-0.5866-0.19150.07910.26010.0402-0.08910.2049-0.02330.19-58.219210.48934.6566
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 135 through 247 )
2X-RAY DIFFRACTION2chain A and (resid 248 through 303 )
3X-RAY DIFFRACTION3chain A and (resid 304 through 382 )
4X-RAY DIFFRACTION4chain A and (resid 383 through 497 )
5X-RAY DIFFRACTION5chain B and (resid 135 through 199 )
6X-RAY DIFFRACTION6chain B and (resid 200 through 365 )
7X-RAY DIFFRACTION7chain B and (resid 366 through 497 )

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