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- PDB-8hch: Crystal structure of mTREX1-Uridine complex -

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Basic information

Entry
Database: PDB / ID: 8hch
TitleCrystal structure of mTREX1-Uridine complex
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / Uridine
Function / homology
Function and homology information


cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / : / immune complex formation / organ or tissue specific immune response / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation ...cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / : / immune complex formation / organ or tissue specific immune response / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / DNA exonuclease activity / DNA modification / regulation of lipid biosynthetic process / heart process / regulation of fatty acid metabolic process / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / regulation of type I interferon production / regulation of lysosome organization / 3'-5'-DNA exonuclease activity / regulation of cellular respiration / MutLalpha complex binding / regulation of tumor necrosis factor production / macrophage activation involved in immune response / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of metabolic process / DNA binding, bending / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / type I interferon-mediated signaling pathway / WW domain binding / DNA metabolic process / regulation of innate immune response / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / kidney development / generation of precursor metabolites and energy / determination of adult lifespan / cellular response to reactive oxygen species / establishment of protein localization / cellular response to gamma radiation / protein-DNA complex / cellular response to UV / single-stranded DNA binding / regulation of gene expression / cellular response to oxidative stress / double-stranded DNA binding / regulation of inflammatory response / defense response to virus / adaptive immune response / DNA replication / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
URIDINE / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHsiao, Y.Y. / Huang, K.W. / Wu, C.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 111-2636-B-A49-006 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.
Authors: Huang, K.W. / Wu, C.Y. / Toh, S.I. / Liu, T.C. / Tu, C.I. / Lin, Y.H. / Cheng, A.J. / Kao, Y.T. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,86312
Polymers109,7894
Non-polymers1,0748
Water8,251458
1
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4316
Polymers54,8942
Non-polymers5374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-16 kcal/mol
Surface area18000 Å2
2
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4316
Polymers54,8942
Non-polymers5374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-16 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.632, 81.149, 93.653
Angle α, β, γ (deg.)90.000, 103.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Three-prime repair exonuclease 1 / 3'-5' exonuclease TREX1


Mass: 27447.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.2% w/v Cytidine, 0.2% w/v Inosine, 0.2% w/v Ribavirin, 0.2% w/v Thymidine, 0.2% w/v Uridine, 0.1M Imidazole, 0.1M MES monohydrate (acid), pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 66457 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Χ2: 1.448 / Net I/σ(I): 12.4 / Num. measured all: 285244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.49532830.7250.280.5720.69299.6
2.03-2.073.80.45332860.8170.2650.5280.91299.3
2.07-2.113.80.39233040.7930.2250.4540.83899.3
2.11-2.1540.31932690.8820.1770.3660.78599.7
2.15-2.24.10.29133460.9020.1610.3340.82499.5
2.2-2.253.80.29233360.8770.1680.3381.13899.4
2.25-2.314.10.23332420.930.1280.2681.04399.3
2.31-2.374.40.18933360.9670.10.2140.946100
2.37-2.444.40.17233230.9720.0910.1951.00399.9
2.44-2.524.50.14433500.9790.0760.1631.09199.9
2.52-2.614.50.1233370.9850.0630.1361.19599.9
2.61-2.714.50.11133330.9850.0590.1261.44399.9
2.71-2.844.50.08933290.9920.0460.11.42999.9
2.84-2.994.60.07433090.9940.0380.0841.58699.9
2.99-3.174.60.0633410.9960.0310.0681.89199.8
3.17-3.424.60.0533430.9980.0260.0571.9899.7
3.42-3.764.50.04533420.9980.0230.0512.2999.4
3.76-4.314.60.0433160.9980.0210.0462.26899.5
4.31-5.424.50.0433680.9970.0210.0462.41699.5
5.42-304.10.03833640.9970.0220.0442.55297.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YWS

5yws


Resolution: 2→24.69 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 5114 7.72 %
Rwork0.187 61161 -
obs0.1901 66275 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.55 Å2 / Biso mean: 46.4932 Å2 / Biso min: 18.58 Å2
Refinement stepCycle: final / Resolution: 2→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 140 438 7335
Biso mean--45.56 45.58 -
Num. residues----873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.28381820.255619992181100
2.02-2.050.2791730.254720402213100
2.05-2.070.30881680.25292005217399
2.07-2.10.2811830.24332001218499
2.1-2.130.25061560.232120582214100
2.13-2.150.26211830.212219912174100
2.15-2.190.25461700.216520422212100
2.19-2.220.25681710.221520282199100
2.22-2.250.26021840.23062045222999
2.25-2.290.25071690.21051998216799
2.29-2.330.25991680.208420342202100
2.33-2.370.2521580.199820512209100
2.37-2.420.22151500.212220552205100
2.42-2.470.23931700.204220342204100
2.47-2.520.27571770.200920492226100
2.52-2.580.24971740.197820342208100
2.58-2.640.23331530.187220552208100
2.64-2.710.25881750.200320502225100
2.71-2.790.23491550.209220562211100
2.79-2.880.25941580.197820402198100
2.88-2.990.23551650.203620502215100
2.99-3.110.22032130.189420252238100
3.11-3.250.25881520.199120552207100
3.25-3.420.22811760.185620392215100
3.42-3.630.24791710.17882032220399
3.63-3.910.18231710.164520702241100
3.91-4.30.19151880.149920062194100
4.3-4.920.1761570.139120842241100
4.92-6.180.19861760.17562074225099
6.18-24.690.22451680.18292061222997
Refinement TLS params.Method: refined / Origin x: 35.4128 Å / Origin y: -16.9027 Å / Origin z: 24.6255 Å
111213212223313233
T0.2201 Å2-0.0067 Å20.0016 Å2-0.2107 Å20.0379 Å2--0.2206 Å2
L0.1123 °2-0.0871 °2-0.0507 °2-0.5799 °20.4761 °2--0.3433 °2
S-0.0392 Å °0.0035 Å °0.0043 Å °-0.0538 Å °0.0326 Å °0.0374 Å °-0.0394 Å °0.0071 Å °0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 234
2X-RAY DIFFRACTION1allB10 - 234
3X-RAY DIFFRACTION1allC10 - 234
4X-RAY DIFFRACTION1allD10 - 234
5X-RAY DIFFRACTION1allF1 - 4
6X-RAY DIFFRACTION1allS1 - 438
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1

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