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- PDB-8hcd: Crystal structure of mTREX1-DNA product complex (dNMP) -

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Basic information

Entry
Database: PDB / ID: 8hcd
TitleCrystal structure of mTREX1-DNA product complex (dNMP)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / dCMP / dGMP
Function / homology
Function and homology information


immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / MutLalpha complex binding / WW domain binding / heart process / regulation of protein complex stability / cellular response to hydroxyurea / regulation of type I interferon production / lymphoid progenitor cell differentiation / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / DNA binding, bending / DNA duplex unwinding / regulation of innate immune response / regulation of glycolytic process / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / 3'-5' exonuclease activity / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / DNA damage checkpoint signaling / generation of precursor metabolites and energy / kidney development / determination of adult lifespan / protein-DNA complex / cellular response to gamma radiation / establishment of protein localization / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / defense response to virus / DNA replication / adaptive immune response / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / endoplasmic reticulum membrane / 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
: / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / 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
B: Three-prime repair exonuclease 1
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
E: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,03017
Polymers119,5084
Non-polymers1,52213
Water14,124784
1
B: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4658
Polymers59,7542
Non-polymers7126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-47 kcal/mol
Surface area18110 Å2
MethodPISA
2
C: Three-prime repair exonuclease 1
E: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5649
Polymers59,7542
Non-polymers8117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-60 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.680, 81.284, 93.209
Angle α, β, γ (deg.)90.000, 103.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules BCDE

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


Mass: 29876.902 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

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Non-polymers , 5 types, 797 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Mass: 307.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / Deoxyguanosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.99 % / Description: 50.09
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 66088 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.073 / Χ2: 1.505 / Net I/σ(I): 11.8 / Num. measured all: 288513
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.073.90.46865770.964199.3
2.07-2.1540.36665380.978199.6
2.15-2.254.10.31966131.274199.4
2.25-2.374.20.22165251.067199.4
2.37-2.524.40.16766351.117199.8
2.52-2.714.50.11765971.229199.8
2.71-2.994.70.08366221.368199.9
2.99-3.424.70.06366422.062199.9
3.42-4.314.50.05166452.789199.9
4.31-304.70.03466941.887198.6

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YWS

5yws


Resolution: 2→29.292 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 5151 7.8 %
Rwork0.1951 60847 -
obs0.1986 65998 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.39 Å2 / Biso mean: 40.9708 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 2→29.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 119 772 7813
Biso mean--40.5 42.6 -
Num. residues----898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02280.32861510.293194595
2.0228-2.04650.31061540.2852203399
2.0465-2.07150.34731480.2881205699
2.0715-2.09770.29641730.2854199399
2.0977-2.12530.29991670.26682026100
2.1253-2.15440.30271620.25142025100
2.1544-2.18520.28341730.26462025100
2.1852-2.21780.31791420.25622030100
2.2178-2.25240.31271740.2734205299
2.2524-2.28930.31971850.2432196499
2.2893-2.32880.27051400.22882076100
2.3288-2.37110.27361820.21711990100
2.3711-2.41670.28972010.21972014100
2.4167-2.4660.251720.21182016100
2.466-2.51960.25241720.21732058100
2.5196-2.57820.26991660.21212003100
2.5782-2.64260.24641740.20782042100
2.6426-2.7140.27532050.20462023100
2.714-2.79380.23091810.20282005100
2.7938-2.88390.26861700.19542037100
2.8839-2.98690.24971830.19932027100
2.9869-3.10640.23291910.19652035100
3.1064-3.24760.22141740.1932034100
3.2476-3.41860.22851550.18582058100
3.4186-3.63240.24491810.17582031100
3.6324-3.91220.2131850.16042052100
3.9122-4.30480.19471690.15012035100
4.3048-4.92520.17851600.13612085100
4.9252-6.19560.19711910.16832064100
6.1956-29.2920.21931700.1735201396
Refinement TLS params.Method: refined / Origin x: 27.9534 Å / Origin y: -4.082 Å / Origin z: 24.7275 Å
111213212223313233
T0.1967 Å2-0.0061 Å2-0.0306 Å2-0.1528 Å20.0095 Å2--0.2242 Å2
L0.4502 °20.2139 °2-0.1565 °2-0.4653 °2-0.0129 °2--0.7883 °2
S0.0084 Å °0.0323 Å °-0.0092 Å °-0.0569 Å °0.0121 Å °0.0294 Å °-0.0579 Å °-0.0249 Å °-0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 3
2X-RAY DIFFRACTION1allB8 - 234
3X-RAY DIFFRACTION1allB800
4X-RAY DIFFRACTION1allC5 - 236
5X-RAY DIFFRACTION1allC301
6X-RAY DIFFRACTION1allD4 - 234
7X-RAY DIFFRACTION1allE9 - 235
8X-RAY DIFFRACTION1allJ1
9X-RAY DIFFRACTION1allL1
10X-RAY DIFFRACTION1allM1
11X-RAY DIFFRACTION1allN1
12X-RAY DIFFRACTION1allO1
13X-RAY DIFFRACTION1allK1
14X-RAY DIFFRACTION1allP1
15X-RAY DIFFRACTION1allG1
16X-RAY DIFFRACTION1allS1 - 780

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