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- PDB-4f9e: Cyclic di-GMP Sensing via the Innate Immune Signaling Protein STING -

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Basic information

Entry
Database: PDB / ID: 4f9e
TitleCyclic di-GMP Sensing via the Innate Immune Signaling Protein STING
ComponentsTransmembrane protein 173
KeywordsPROTEIN BINDING / STING / ERIS / MITA / Stimulator of interferon genes protein / innate immunity 5helix and 5 beta strand
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / protein localization to endoplasmic reticulum / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / STING mediated induction of host immune responses / cyclic-di-GMP binding / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / reticulophagy / pattern recognition receptor signaling pathway / 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 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / positive regulation of DNA-binding transcription factor activity / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein complex oligomerization / regulation of inflammatory response / 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 / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / 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
Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.75 Å
AuthorsKabaleeswaran, V. / Wu, H.
CitationJournal: Mol.Cell / Year: 2012
Title: Cyclic di-GMP Sensing via the Innate Immune Signaling Protein STING.
Authors: Yin, Q. / Tian, Y. / Kabaleeswaran, V. / Jiang, X. / Tu, D. / Eck, M.J. / Chen, Z.J. / Wu, H.
History
DepositionMay 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protein 173


Theoretical massNumber of molelcules
Total (without water)29,8481
Polymers29,8481
Non-polymers00
Water37821
1
A: Transmembrane protein 173

A: Transmembrane protein 173


Theoretical massNumber of molelcules
Total (without water)59,6972
Polymers59,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1470 Å2
ΔGint-16 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 61.400, 118.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

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


Mass: 29848.463 Da / Num. of mol.: 1 / Fragment: C-terminal Domain (unp residues 139-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86WV6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.05 Å3/Da / Density % sol: 34.15 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionRedundancy: 14.1 % / Av σ(I) over netI: 13.8 / Number: 90342 / Rsym value: 0.042 / D res high: 2.75 Å / D res low: 35.043 Å / Num. obs: 6389 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
12.335.0495.610.0180.01810.4
8.712.399.110.020.0211.8
7.18.710010.0230.02312.8
6.157.110010.0270.02713.4
5.56.1510010.0310.03113.4
5.025.510010.0280.02814.3
4.655.0210010.0270.02713.7
4.354.6510010.0310.03114.5
4.14.3510010.0330.03313.7
3.894.199.710.0360.03614.2
3.713.8910010.0430.04314.6
3.553.7199.810.0560.05613.5
3.413.5510010.0710.07114.6
3.293.4110010.0890.08914.1
3.183.2910010.1320.13214
3.073.1810010.150.1514.7
2.983.0710010.2070.20715
2.92.9810010.2720.27214.6
2.822.910010.3560.35614.6
2.752.8210010.5210.52115
ReflectionResolution: 2.75→35.001 Å / Num. all: 6371 / Num. obs: 6371 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Rsym value: 0.038 / Net I/σ(I): 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.75-2.828.60.4561.739324580.456100
2.82-2.98.30.3062.536804410.306100
2.9-2.988.40.2463.136104290.246100
2.98-3.078.70.1824.236904250.182100
3.07-3.188.50.1335.734584070.133100
3.18-3.2980.1116.931473930.111100
3.29-3.418.20.0789.832383960.078100
3.41-3.558.50.06311.929983540.063100
3.55-3.717.80.05213.928633650.05299.8
3.71-3.898.40.03917.828583400.039100
3.89-4.18.20.03221.927133300.03299.7
4.1-4.357.90.0322.824583130.03100
4.35-4.658.40.0282324542920.028100
4.65-5.027.90.02426.721852780.024100
5.02-5.58.20.02623.621692640.026100
5.5-6.157.80.02919.218492380.029100
6.15-7.17.70.0252415942080.025100
7.1-8.77.40.02126.314331930.02199.9
8.7-12.36.80.01733.310441540.01799.1
12.3-35.00160.01541.3558930.01596

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.75→35.001 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.79 / SU ML: 0.5 / σ(F): 1.36 / σ(I): 2 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 298 4.69 %RANDOM
Rwork0.2117 ---
obs0.2138 6371 99.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.573 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 116.34 Å2 / Biso mean: 68.0824 Å2 / Biso min: 36.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.9937 Å20 Å2-0 Å2
2--2.9937 Å2-0 Å2
3----5.9875 Å2
Refinement stepCycle: LAST / Resolution: 2.75→35.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 0 21 1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091402
X-RAY DIFFRACTIONf_angle_d1.2021903
X-RAY DIFFRACTIONf_chiral_restr0.076212
X-RAY DIFFRACTIONf_plane_restr0.005250
X-RAY DIFFRACTIONf_dihedral_angle_d15.869518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7501-3.02670.45151360.314826652801
3.0267-3.46430.27041240.245126832807
3.4643-4.36340.28111320.188126832815
4.3634-35.00380.20811340.197326692803

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