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- PDB-4jc5: Immune activator bound to receptor -

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Basic information

Entry
Database: PDB / ID: 4jc5
TitleImmune activator bound to receptor
ComponentsTransmembrane protein 173
KeywordsIMMUNE SYSTEM / Innate immune receptor
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 / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated 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 / protein localization to endoplasmic reticulum / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / 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 / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / peroxisome / 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 / lysosomal membrane / 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 / plasma membrane / cytoplasm / cytosol
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
(9-oxoacridin-10(9H)-yl)acetic acid / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsDeimling, T. / Hopfner, K.P.
CitationJournal: Embo J. / Year: 2013
Title: Species-specific detection of the antiviral small-molecule compound CMA by STING.
Authors: Cavlar, T. / Deimling, T. / Ablasser, A. / Hopfner, K.P. / Hornung, V.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transmembrane protein 173
B: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3214
Polymers45,8142
Non-polymers5072
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-21 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.540, 108.540, 100.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Transmembrane protein 173 / Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / ...Endoplasmic reticulum interferon stimulator / ERIS / Mediator of IRF3 activation / MMITA / Stimulator of interferon genes protein / mSTING


Mass: 22907.090 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain (LBD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem173, Eris Mita, Mpys, Sting / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TBT3
#2: Chemical ChemComp-1K5 / (9-oxoacridin-10(9H)-yl)acetic acid


Mass: 253.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 1.65 M ammonium sulphate, 2 % PEG 400 (v/v), saturating amounts of CMA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2012
Details: Sagittally horizontal focussing crystal (Fixed-exit LN2 cooled Double Crystal Monochromator, Si(111)), meridionally vertical focussing mirror (Rh coated meridionally focussing mirror)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 11527 / Num. obs: 11448 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.75→2.91 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→34.378 Å / SU ML: 0.44 / σ(F): 2.01 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 572 5 %random by xdsconv
Rwork0.2095 ---
obs0.2109 11444 99.31 %-
all-11527 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→34.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 38 32 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073085
X-RAY DIFFRACTIONf_angle_d1.1594170
X-RAY DIFFRACTIONf_dihedral_angle_d20.3441178
X-RAY DIFFRACTIONf_chiral_restr0.076449
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.0260.37121430.28212707X-RAY DIFFRACTION99
3.026-3.46350.26511430.24142719X-RAY DIFFRACTION100
3.4635-4.36230.22631440.19622742X-RAY DIFFRACTION100
4.3623-34.38030.21611420.1982704X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -36.2121 Å / Origin y: 0.4779 Å / Origin z: 14.2246 Å
111213212223313233
T0.397 Å2-0.1708 Å2-0.0483 Å2-0.3741 Å20.0081 Å2--0.3436 Å2
L3.5437 °22.1864 °2-0.4633 °2-8.4475 °2-2.5285 °2--2.8483 °2
S0.0228 Å °-0.0584 Å °0.1693 Å °0.0467 Å °-0.2354 Å °-0.368 Å °-0.5823 Å °0.5336 Å °0.1508 Å °
Refinement TLS groupSelection details: ALL

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