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- PDB-5gs5: Crystal structure of apo rat STING -

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Basic information

Entry
Database: PDB / ID: 5gs5
TitleCrystal structure of apo rat STING
ComponentsStimulator of interferon genes protein
KeywordsIMMUNE SYSTEM / rat STING
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 / pattern recognition receptor signaling pathway ...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 / pattern recognition receptor signaling pathway / Neutrophil degranulation / cytoplasmic pattern recognition receptor signaling pathway / cellular response to exogenous dsRNA / autophagosome membrane / antiviral innate immune response / positive regulation of macroautophagy / cellular response to organic cyclic compound / autophagosome assembly / autophagosome / positive regulation of type I interferon production / 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 / positive regulation of DNA-binding transcription factor activity / peroxisome / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / regulation of gene expression / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / 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 / cytoplasm / cytosol
Similarity search - Function
Stimulator of interferon genes protein / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / Transmembrane protein 173 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
#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 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Stimulator of interferon genes protein
D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,16213
Polymers101,2984
Non-polymers8659
Water10,809600
1
A: Stimulator of interferon genes protein
hetero molecules

C: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1297
Polymers50,6492
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area3010 Å2
ΔGint-19 kcal/mol
Surface area21330 Å2
MethodPISA
2
B: Stimulator of interferon genes protein
hetero molecules

D: Stimulator of interferon genes protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0336
Polymers50,6492
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area3050 Å2
ΔGint-35 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.290, 75.510, 87.640
Angle α, β, γ (deg.)90.000, 115.350, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-564-

HOH

21B-650-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYGLNGLNchain AAA136 - 33520 - 219
2SERSERALAALAchain BBB137 - 34121 - 225
3HISHISALAALAchain CCC126 - 34110 - 225
4SERSERALAALAchain DDD127 - 33911 - 223

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Components

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


Mass: 25324.426 Da / Num. of mol.: 4 / Fragment: UNP residues 140-337
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200mM NaCl, 20mM MES pH6.5

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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: CCD / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 70041 / % possible obs: 98.8 % / Redundancy: 3.75 % / Net I/σ(I): 12.54
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.23 / % possible all: 98.2

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Processing

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

4loj


Resolution: 1.84→42.728 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.06
RfactorNum. reflection% reflection
Rfree0.2219 3529 5.04 %
Rwork0.1812 --
obs0.1833 70033 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 25.37 Å2 / Biso min: 3.72 Å2
Refinement stepCycle: final / Resolution: 1.84→42.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6579 0 45 600 7224
Biso mean--34.3 32.57 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086749
X-RAY DIFFRACTIONf_angle_d1.2929126
X-RAY DIFFRACTIONf_chiral_restr0.099973
X-RAY DIFFRACTIONf_plane_restr0.0061218
X-RAY DIFFRACTIONf_dihedral_angle_d13.7442520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4020X-RAY DIFFRACTION18.293TORSIONAL
12B4020X-RAY DIFFRACTION18.293TORSIONAL
13C4020X-RAY DIFFRACTION18.293TORSIONAL
14D4020X-RAY DIFFRACTION18.293TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86520.37261460.32062630277699
1.8652-1.89190.37771310.29912603273498
1.8919-1.92010.29141290.26062656278599
1.9201-1.95010.28361140.24112632274698
1.9501-1.98210.28371250.22612655278098
1.9821-2.01620.26461430.22112613275699
2.0162-2.05290.29851470.22042644279198
2.0529-2.09240.26711090.21062676278599
2.0924-2.13510.27991380.20332654279299
2.1351-2.18150.22821570.19362652280999
2.1815-2.23230.2611370.19012626276399
2.2323-2.28810.2271560.18142637279399
2.2881-2.350.2291290.17792657278699
2.35-2.41910.22051530.1772665281899
2.4191-2.49720.20251760.18092619279599
2.4972-2.58640.2351400.18482683282399
2.5864-2.68990.21171540.17572652280699
2.6899-2.81230.2171430.17572705284899
2.8123-2.96060.2111560.16926402796100
2.9606-3.1460.21621490.1652696284599
3.146-3.38880.16861270.15992659278699
3.3888-3.72970.19431400.15162694283499
3.7297-4.2690.17211380.14262684282299
4.269-5.37680.18441360.15192706284299
5.3768-42.73940.21961560.18942766292299
Refinement TLS params.Method: refined / Origin x: -10.9154 Å / Origin y: 67.7124 Å / Origin z: 22.9398 Å
111213212223313233
T0.108 Å20.0151 Å20.0088 Å2-0.149 Å2-0.0071 Å2--0.1428 Å2
L-0.0022 °20.0508 °20.0545 °2-0.0575 °20.0168 °2--0.0882 °2
S-0.003 Å °0.0196 Å °-0.0017 Å °-0.0412 Å °0.0065 Å °-0.0274 Å °-0.0122 Å °0.0089 Å °-0.0042 Å °
Refinement TLS groupSelection details: all

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