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- PDB-5grm: Crystal structure of rat STING in complex with cyclic GMP-AMP wit... -

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Basic information

Entry
Database: PDB / ID: 5grm
TitleCrystal structure of rat STING in complex with cyclic GMP-AMP with 2'5'and 3'5'phosphodiester linkage(2'3'-cGAMP)
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / Rat STING / 2'3'-cGAMP
Function / homology
Function and homology information


STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / STING complex / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / Neutrophil degranulation ...STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / IRF3-mediated induction of type I IFN / Regulation of innate immune responses to cytosolic DNA / STING complex / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / Neutrophil degranulation / pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / autophagosome assembly / cellular response to organic cyclic compound / positive regulation of type I interferon production / autophagosome / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / protein serine/threonine kinase activator activity / molecular function activator activity / peroxisome / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / positive regulation of protein binding / regulation of inflammatory response / regulation of gene expression / defense response to virus / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / endosome / Golgi membrane / innate immune response / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #5200 / Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cGAMP / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhang, H. / Han, M.J. / Tao, J.L. / Ye, Z.Y. / Du, X.X. / Deng, M.J. / Zhang, X.Y. / Li, L.F. / Jiang, Z.F. / Su, X.D.
Citation
Journal: To Be Published
Title: Crystal structure of rat STING in complex with cyclic GMP-AMP with 2'5'and 3'5'phosphodiester linkage(2'3'-cGAMP)
Authors: Zhang, H. / Han, M.J. / Tao, J.L. / Ye, Z.Y. / Du, X.X. / Deng, M.J. / Zhang, X.Y. / Li, L.F. / Jiang, Z.F. / Su, X.D.
#1: Journal: Sci Rep. / Year: 2015
Title: Rat and human STINGs profile similarly towards anticancer/antiviral compounds
Authors: Zhang, H. / Han, M.J. / Tao, J.L. / Ye, Z.Y. / Du, X.X. / Deng, M.J. / Zhang, X.Y. / Li, L.F. / Jiang, Z.F. / Su, X.D.
History
DepositionAug 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stimulator of interferon genes protein
B: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5463
Polymers47,8722
Non-polymers6741
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-25 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.200, 77.200, 152.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stimulator of interferon genes protein / / rSTING / Transmembrane protein 173


Mass: 23935.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tmem173, Sting / Production host: Escherichia coli (E. coli) / References: UniProt: F1M391
#2: 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.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8M (NH4)2SO4, 0.1M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 67310 / % possible obs: 99.8 % / Redundancy: 7.14 % / Net I/σ(I): 20.12
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 6032 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOJ

4loj


Resolution: 1.55→42.378 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 3407 5.06 %
Rwork0.1809 --
obs0.1815 67309 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→42.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 45 406 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0353133
X-RAY DIFFRACTIONf_angle_d2.3274242
X-RAY DIFFRACTIONf_dihedral_angle_d15.2921172
X-RAY DIFFRACTIONf_chiral_restr0.187452
X-RAY DIFFRACTIONf_plane_restr0.01557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57220.23251330.23632631X-RAY DIFFRACTION100
1.5722-1.59560.2291160.2222641X-RAY DIFFRACTION100
1.5956-1.62060.23531410.21372614X-RAY DIFFRACTION100
1.6206-1.64710.22031180.21672657X-RAY DIFFRACTION100
1.6471-1.67550.20831350.21732645X-RAY DIFFRACTION100
1.6755-1.7060.23561420.21672636X-RAY DIFFRACTION100
1.706-1.73880.24631380.20592609X-RAY DIFFRACTION100
1.7388-1.77430.21311450.20232625X-RAY DIFFRACTION100
1.7743-1.81290.20391330.2052650X-RAY DIFFRACTION100
1.8129-1.85510.23741500.19762647X-RAY DIFFRACTION100
1.8551-1.90150.20061460.18712633X-RAY DIFFRACTION100
1.9015-1.95290.22771390.19152633X-RAY DIFFRACTION100
1.9529-2.01030.19611370.19292635X-RAY DIFFRACTION100
2.0103-2.07520.20691530.18662647X-RAY DIFFRACTION100
2.0752-2.14940.19081560.18122651X-RAY DIFFRACTION100
2.1494-2.23540.20381430.18222644X-RAY DIFFRACTION100
2.2354-2.33720.21861540.17752659X-RAY DIFFRACTION100
2.3372-2.46040.17691500.18842656X-RAY DIFFRACTION100
2.4604-2.61450.20121400.1862693X-RAY DIFFRACTION100
2.6145-2.81630.21621340.18452678X-RAY DIFFRACTION100
2.8163-3.09970.19231530.18922704X-RAY DIFFRACTION100
3.0997-3.5480.1571390.16442711X-RAY DIFFRACTION99
3.548-4.46940.16381550.14632725X-RAY DIFFRACTION99
4.4694-42.3940.16941570.16452878X-RAY DIFFRACTION98

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