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- PDB-8hcc: Crystal structure of mTREX1-RNA product complex (AMP) -

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Basic information

Entry
Database: PDB / ID: 8hcc
TitleCrystal structure of mTREX1-RNA product complex (AMP)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / AMP
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
ADENOSINE 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
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)121,20621
Polymers119,5084
Non-polymers1,69817
Water11,674648
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61411
Polymers59,7542
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-84 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,59110
Polymers59,7542
Non-polymers8388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-73 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.197, 86.433, 75.218
Angle α, β, γ (deg.)90.000, 97.600, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 22, 2015
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: 61417 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 1.71 / Net I/σ(I): 12.2 / Num. measured all: 252782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0740.47760880.7970.2730.5511.35899.9
2.07-2.1540.34761590.8840.1980.41.40999.9
2.15-2.254.10.2861000.9190.1590.3231.439100
2.25-2.374.10.21260960.9560.120.2441.43299.9
2.37-2.524.10.16461160.9750.0920.1891.47699.9
2.52-2.714.20.12361370.9850.0690.1411.61399.8
2.71-2.994.20.08761490.9930.0480.11.73199.9
2.99-3.424.20.05761620.9960.0310.0651.999.9
3.42-4.314.10.04761510.9970.0260.0542.486100
4.31-304.10.03962590.9970.0220.0452.21299.7

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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→27.164 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 4759 7.8 %
Rwork0.1667 56225 -
obs0.1701 60984 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.18 Å2 / Biso mean: 36.1577 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2→27.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 153 648 7802
Biso mean--38.66 37.38 -
Num. residues----907
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.28071710.22891824100
2.0227-2.04650.27321660.22561859100
2.0465-2.07150.24691630.21041881100
2.0715-2.09770.23851640.20321865100
2.0977-2.12530.22641640.19911837100
2.1253-2.15440.22951310.19491922100
2.1544-2.18510.22831360.18951842100
2.1851-2.21770.23691650.20031897100
2.2177-2.25240.24421590.19191864100
2.2524-2.28930.23791510.17691887100
2.2893-2.32870.23331530.17751846100
2.3287-2.37110.20711750.17621855100
2.3711-2.41660.23061340.17141895100
2.4166-2.46590.22421630.17531858100
2.4659-2.51950.23671440.17191880100
2.5195-2.57810.21851420.16761861100
2.5781-2.64250.22171700.16831900100
2.6425-2.71390.21811520.17891861100
2.7139-2.79370.22881720.17221880100
2.7937-2.88370.21041770.17671842100
2.8837-2.98670.2111290.17221906100
2.9867-3.10610.21951680.17231882100
3.1061-3.24730.23941530.17431870100
3.2473-3.41810.20411610.16611880100
3.4181-3.63180.18271560.15541867100
3.6318-3.91150.19241690.14951885100
3.9115-4.30370.17081720.13251865100
4.3037-4.92330.18951610.12631894100
4.9233-6.19070.21331810.16011891100
6.1907-27.1640.18131570.1676192999
Refinement TLS params.Method: refined / Origin x: 12.3214 Å / Origin y: 1.0209 Å / Origin z: 29.5066 Å
111213212223313233
T0.2049 Å20.0031 Å20.0211 Å2-0.2068 Å2-0.0023 Å2--0.2331 Å2
L0.222 °20.0109 °20.2627 °2-0.0322 °20.0747 °2--0.4413 °2
S-0.0122 Å °-0.0567 Å °-0.0005 Å °-0.0016 Å °0.0179 Å °-0.0175 Å °-0.0374 Å °0.0042 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 234
2X-RAY DIFFRACTION1allB5 - 234
3X-RAY DIFFRACTION1allC5 - 235
4X-RAY DIFFRACTION1allD5 - 234
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allL1
13X-RAY DIFFRACTION1allM1
14X-RAY DIFFRACTION1allN1
15X-RAY DIFFRACTION1allO1
16X-RAY DIFFRACTION1allP1
17X-RAY DIFFRACTION1allS1 - 649
18X-RAY DIFFRACTION1allQ1
19X-RAY DIFFRACTION1allR1
20X-RAY DIFFRACTION1allT1
21X-RAY DIFFRACTION1allU1
22X-RAY DIFFRACTION1allV1

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