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- PDB-4f5y: Crystal structure of human STING CTD complex with C-di-GMP -

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Basic information

Entry
Database: PDB / ID: 4f5y
TitleCrystal structure of human STING CTD complex with C-di-GMP
ComponentsTransmembrane protein 173
KeywordsIMMUNE SYSTEM / Innate immunity / STING / C-di-GMP
Function / homology
Function and homology information


STING complex / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway ...STING complex / STING mediated induction of host immune responses / STAT6-mediated induction of chemokines / serine/threonine protein kinase complex / protein localization to endoplasmic reticulum / 2',3'-cyclic GMP-AMP binding / proton channel activity / cyclic-di-GMP binding / pattern recognition receptor signaling pathway / cGAS/STING signaling pathway / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / reticulophagy / cellular response to exogenous dsRNA / cellular response to organic cyclic compound / protein complex oligomerization / positive regulation of type I interferon production / positive regulation of macroautophagy / autophagosome membrane / autophagosome assembly / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / antiviral innate immune response / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of interferon-beta production / autophagosome / Regulation of innate immune responses to cytosolic DNA / secretory granule membrane / positive regulation of DNA-binding transcription factor activity / cytoplasmic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / peroxisome / 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
Chem-C2E / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsGu, L. / Shang, G. / Zhu, D. / Li, N. / Zhang, J. / Zhu, C. / Lu, D. / Liu, C. / Yu, Q. / Zhao, Y. / Xu, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structures of STING protein reveal basis for recognition of cyclic di-GMP
Authors: Shang, G. / Zhu, D. / Li, N. / Zhang, J. / Zhu, C. / Lu, D. / Liu, C. / Yu, Q. / Zhao, Y. / Xu, S. / Gu, L.
History
DepositionMay 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
B: Transmembrane protein 173
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2505
Polymers54,4792
Non-polymers7713
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-29 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.145, 81.438, 91.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 27239.615 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 149-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM173, ERIS, MITA, STING / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86WV6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATURAL VARIANT AT THIS POSITION

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 8000, 0.08M sodium cacodylate pH6.5, 0.16M calcium acetate and 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97891 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2011
RadiationMonochromator: SAGITTALLY FOCUSED Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.396→50 Å / Num. all: 22031 / Num. obs: 22031 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 25.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.4-2.497.40.5013.8921500.501100
5.17-506.90.0454.9623690.0499.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.396→39.836 Å / SU ML: 0.66 / σ(F): 1.36 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1126 5.13 %RANDOM
Rwork0.2115 ---
all0.2146 21966 --
obs0.2146 21966 99.7 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.482 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3502 Å2-0 Å20 Å2
2---6.94 Å2-0 Å2
3---12.2902 Å2
Refinement stepCycle: LAST / Resolution: 2.396→39.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 48 138 3292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083216
X-RAY DIFFRACTIONf_angle_d1.1954370
X-RAY DIFFRACTIONf_dihedral_angle_d17.9561198
X-RAY DIFFRACTIONf_chiral_restr0.081478
X-RAY DIFFRACTIONf_plane_restr0.005574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3965-2.50550.30211250.2394252898
2.5055-2.63760.31511530.24122542100
2.6376-2.80280.32431450.23342575100
2.8028-3.01920.25391520.21422559100
3.0192-3.32290.29011510.19822588100
3.3229-3.80340.26531290.20442629100
3.8034-4.79050.2381320.18332651100
4.7905-39.84170.2831390.23042768100

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