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

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Basic information

Entry
Database: PDB / ID: 6ukm
TitleSTING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound MSA-2
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-QAD / 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: 1.74 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 5, 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7512
Polymers34,4571
Non-polymers2941
Water2,000111
1
A: fusion protein of Ubiquitin-like protein SMT3 and Stimulator of interferon protein c-terminal domain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)69,5024
Polymers68,9132
Non-polymers5892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area4090 Å2
ΔGint-17 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.610, 61.150, 36.200
Angle α, β, γ (deg.)90.000, 103.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-562-

HOH

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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.: 1 / 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-QAD / 4-(5,6-dimethoxy-1-benzothiophen-2-yl)-4-oxobutanoic acid


Mass: 294.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.54 Å3/Da / Density % sol: 20.05 % / Mosaicity: 0.45 °
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: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.738→47.9 Å / Num. obs: 19712 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.15 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 12.1
Reflection shellResolution: 1.738→1.744 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. measured all: 10069 / Num. unique obs: 3031 / CC1/2: 0.797 / Rpim(I) all: 0.394 / Rrim(I) all: 0.73 / Net I/σ(I) obs: 2.1 / % possible all: 94.5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4KSY

4ksy


Resolution: 1.74→47.9 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9514 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 1002 5.1 %RANDOM
Rwork0.1793 ---
obs0.18 19658 91.24 %-
Displacement parametersBiso max: 158.14 Å2 / Biso mean: 38.45 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1-6.5131 Å20 Å2-0.6267 Å2
2---6.0501 Å20 Å2
3----0.463 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: final / Resolution: 1.74→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 34 111 1564
Biso mean--21.62 43.3 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011512HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012065HARMONIC2
LS refinement shellResolution: 1.74→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2714 153 5.06 %
Rwork0.2095 2868 -
all0.2124 3021 -
obs--96.64 %
Refinement TLS params.Method: refined / Origin x: 41.0684 Å / Origin y: 5.5377 Å / Origin z: -18.9822 Å
111213212223313233
T-0.0563 Å2-0.0017 Å2-0.0081 Å2--0.0113 Å20.0168 Å2---0.0169 Å2
L1.5337 °2-0.6716 °2-0.0008 °2-1.2014 °20.0691 °2--0.4399 °2
S-0.056 Å °0.0454 Å °0.204 Å °-0.0789 Å °0.0474 Å °0.1044 Å °-0.0058 Å °-0.1401 Å °0.0086 Å °
Refinement TLS groupSelection details: { A|* }

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