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- PDB-6ukv: STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Co... -

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Basic information

Entry
Database: PDB / ID: 6ukv
TitleSTING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 9
Componentsfusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain
KeywordsIMMUNE SYSTEM / AGONIST / STING (STIMULATOR OF INTERFERON GENES) / TRANSMEMBRANE PROTEIN 173 (TMEM173) / IMMUNE SYSTEM-INHIBITOR COMPLEX / IMMUNE SYSTEM-AGONIST COMPLEX
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / autophagosome membrane / protein sumoylation / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / condensed nuclear chromosome / protein tag activity / mitochondrial outer membrane / nucleotide binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / identical protein binding / nucleus
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues ...: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-QB1 / Stimulator of interferon genes protein / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLesburg, C.A.
CitationJournal: Science / Year: 2020
Title: An orally available non-nucleotide STING agonist with antitumor activity.
Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / ...Authors: Pan, B.S. / Perera, S.A. / Piesvaux, J.A. / Presland, J.P. / Schroeder, G.K. / Cumming, J.N. / Trotter, B.W. / Altman, M.D. / Buevich, A.V. / Cash, B. / Cemerski, S. / Chang, W. / Chen, Y. / Dandliker, P.J. / Feng, G. / Haidle, A. / Henderson, T. / Jewell, J. / Kariv, I. / Knemeyer, I. / Kopinja, J. / Lacey, B.M. / Laskey, J. / Lesburg, C.A. / Liang, R. / Long, B.J. / Lu, M. / Ma, Y. / Minnihan, E.C. / O'Donnell, G. / Otte, R. / Price, L. / Rakhilina, L. / Sauvagnat, B. / Sharma, S. / Tyagarajan, S. / Woo, H. / Wyss, D.F. / Xu, S. / Bennett, D.J. / Addona, G.H.
History
DepositionOct 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain
B: fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1144
Polymers68,9132
Non-polymers1,2012
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-15 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.510, 109.390, 59.150
Angle α, β, γ (deg.)90.000, 95.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain


Mass: 34456.527 Da / Num. of mol.: 2 / Mutation: G230A,R293Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human)
Strain: ATCC 204508 / S288c
Gene: SMT3, YDR510W, D9719.15, STING, LOC340061, hCG_1782396
Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)) / References: UniProt: Q12306, UniProt: A0A2R3XZB7
#2: Chemical ChemComp-QB1 / 4-[6-(3-{[2-(3-carboxypropanoyl)-6-methoxy-1-benzothiophen-5-yl]oxy}propoxy)-5-methoxy-1-benzothiophen-2-yl]-4-oxobutanoic acid


Mass: 600.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H28O10S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.71 Å3/Da / Density % sol: 27.88 % / Mosaicity: 0.08 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→58.855 Å / Num. obs: 40497 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Rsym value: 0.052 / Net I/σ(I): 13.9
Reflection shellResolution: 1.831→1.862 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.1 / Num. measured all: 19958 / Num. unique obs: 5874 / CC1/2: 0.819 / Rpim(I) all: 0.28 / Rrim(I) all: 0.521 / Rsym value: 0.528 / Net I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 6UKM

6ukm


Resolution: 1.83→26.79 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2012 4.97 %RANDOM
Rwork0.189 ---
obs0.19 40481 99.6 %-
Displacement parametersBiso max: 127.69 Å2 / Biso mean: 32.03 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.2771 Å20 Å2-0.5783 Å2
2--0.7466 Å20 Å2
3---0.5306 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.83→26.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 134 289 3259
Biso mean--17.15 40.09 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964148HARMONIC2
LS refinement shellResolution: 1.83→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2723 149 5.14 %
Rwork0.238 2749 -
all0.2396 2898 -
obs--98.25 %

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