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- PDB-4f5e: Crystal structure of ERIS/STING -

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Basic information

Entry
Database: PDB / ID: 4f5e
TitleCrystal structure of ERIS/STING
ComponentsTransmembrane protein 173Stimulator of interferon genes
KeywordsIMMUNE SYSTEM / Receptor
Function / homology
Function and homology information


STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway ...STING complex / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / proton channel activity / 2',3'-cyclic GMP-AMP binding / cyclic-di-GMP binding / STING mediated induction of host immune responses / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / reticulophagy / 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 / 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 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / activation of innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / cytoplasmic vesicle membrane / peroxisome / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / protein complex oligomerization / positive regulation of protein binding / regulation of inflammatory response / 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 / 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 / Resolution: 2.601 Å
AuthorsHuang, Y.H. / Liu, X.Y. / Su, X.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The structural basis for the sensing and binding of cyclic di-GMP by STING
Authors: Huang, Y.H. / Liu, X.Y. / Du, X.X. / Jiang, Z.F. / Su, X.D.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: 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 / 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 / _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

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Assembly

Deposited unit
A: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8622
Polymers28,6231
Non-polymers2381
Water55831
1
A: Transmembrane protein 173
hetero molecules

A: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7234
Polymers57,2472
Non-polymers4772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.820, 60.820, 120.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein Transmembrane protein 173 / Stimulator of interferon genes / 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: 28623.375 Da / Num. of mol.: 1 / Fragment: UNP residues 141-379 / Mutation: G230A
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) / References: UniProt: Q86WV6
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsH232R IS BASED ON REF2 OF DATABASE Q86WV6 (TM173_HUMAN). IT CORRESPONDS TO VARIANT RS1131769.

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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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25.0% PEG 3350, 0.1M Bis-tris pH 6.5, 0.2M NH4-acetate, 5% Glycerol, 0.025% Dichloromethane, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7431 / Num. obs: 7343 / % possible obs: 98.8 % / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.601→19.991 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8194 / SU ML: 0.32 / σ(F): 2 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 732 9.99 %
Rwork0.2115 --
obs0.2158 7324 98.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.91 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 199.78 Å2 / Biso mean: 84.2933 Å2 / Biso min: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.7143 Å2-0 Å2-0 Å2
2--1.7143 Å20 Å2
3----3.4286 Å2
Refinement stepCycle: LAST / Resolution: 2.601→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 15 31 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131541
X-RAY DIFFRACTIONf_angle_d0.9632089
X-RAY DIFFRACTIONf_dihedral_angle_d17.764588
X-RAY DIFFRACTIONf_chiral_restr0.082225
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6006-2.80090.33781430.30571287100
2.8009-3.08180.30221440.26891306100
3.0818-3.52570.31711440.22061296100
3.5257-4.4340.19671470.181132399
4.434-19.99160.251540.2037138097
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)
17.48362.0232-3.52373.3449-2.00775.14150.173-0.342-0.01830.2732-0.01880.1563-0.38080.1222-00.3513-0.0137-0.09770.4237-0.00140.3524-4.5757-5.65615.0695
24.83323.6044-0.1163.59281.2772.05760.57110.0720.10540.66951.19120.7945-0.622-0.7548-1.2121.0658-0.1301-0.11041.5368-0.34911.3882-6.8835-6.49555.724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 151:336 )A151 - 336
2X-RAY DIFFRACTION2( CHAIN A AND RESID 401:401 )A401

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