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- PDB-8hcf: Crystal structure of mTREX1-UMP complex -

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Basic information

Entry
Database: PDB / ID: 8hcf
TitleCrystal structure of mTREX1-UMP complex
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / UMP
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 / MutSalpha complex binding ...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 / regulation of fatty acid metabolic process / regulation of protein complex stability / heart process / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / 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 / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / DNA catabolic process / regulation of immunoglobulin production / regulation of T cell activation / apoptotic cell clearance / DNA binding, bending / regulation of glycolytic process / regulation of metabolic process / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / regulation of innate immune response / WW domain binding / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / blood vessel development / nuclear replication fork / heart morphogenesis / response to UV / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / determination of adult lifespan / cellular response to reactive oxygen species / generation of precursor metabolites and energy / kidney development / establishment of protein localization / cellular response to gamma radiation / protein-DNA complex / cellular response to UV / single-stranded DNA binding / regulation of gene expression / regulation of inflammatory response / cellular response to oxidative stress / double-stranded DNA binding / 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 / cytoplasm / cytosol
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-5'-MONOPHOSPHATE / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6417
Polymers54,7902
Non-polymers8515
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-50 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.031, 85.771, 100.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27395.115 Da / Num. of mol.: 2
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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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: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 73263 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.02 / Rrim(I) all: 0.057 / Χ2: 1.363 / Net I/σ(I): 15.8 / Num. measured all: 558283
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.667.30.4972230.8950.1910.5260.658100
1.66-1.727.40.37172810.9390.1440.3980.7100
1.72-1.87.50.26572110.9690.1020.2850.767100
1.8-1.97.50.18472520.9850.070.1970.886100
1.9-2.027.60.12672700.9940.0480.1351.088100
2.02-2.177.90.08672940.9970.0320.0921.312100
2.17-2.397.90.06673370.9980.0240.071.518100
2.39-2.7480.05173210.9990.0190.0541.814100
2.74-3.457.80.03874260.9990.0140.0412.097100
3.45-307.30.03776480.9990.0140.042.62499.2

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Processing

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

5yws


Resolution: 1.6→23.143 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1789 5741 7.84 %
Rwork0.1522 67445 -
obs0.1543 73186 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135 Å2 / Biso mean: 31.4119 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 1.6→23.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 79 564 4136
Biso mean--54.09 40.39 -
Num. residues----452
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6001-1.61830.20011720.1955218797
1.6183-1.63730.24071850.19632209100
1.6373-1.65730.21221960.19182215100
1.6573-1.67820.22211950.18342221100
1.6782-1.70030.20131890.17542226100
1.7003-1.72360.18821990.16362233100
1.7236-1.74820.18632030.16262201100
1.7482-1.77430.19271840.16092224100
1.7743-1.8020.21381710.16132244100
1.802-1.83150.18711720.1612288100
1.8315-1.86310.22021890.16192200100
1.8631-1.8970.19841800.1582228100
1.897-1.93340.19811990.14682231100
1.9334-1.97290.16031670.14552253100
1.9729-2.01580.16321940.14262231100
2.0158-2.06260.17131760.14592280100
2.0626-2.11420.18362070.13692199100
2.1142-2.17130.16421830.14122247100
2.1713-2.23510.19511920.14232251100
2.2351-2.30720.17752000.13922236100
2.3072-2.38960.15932010.13452252100
2.3896-2.48520.16141980.13562253100
2.4852-2.59810.18271750.13832250100
2.5981-2.73490.15931960.14562250100
2.7349-2.90590.18692180.15892267100
2.9059-3.12980.16121850.16122275100
3.1298-3.44390.19121990.15552272100
3.4439-3.94010.15821910.14182319100
3.9401-4.9560.15172050.12782326100
4.956-23.1430.21532200.1975237799
Refinement TLS params.Method: refined / Origin x: 31.9764 Å / Origin y: -0.0311 Å / Origin z: 19.1493 Å
111213212223313233
T0.1017 Å20.0067 Å20.0026 Å2-0.0992 Å2-0.0007 Å2--0.1357 Å2
L0.3803 °20.0948 °20.0063 °2-0.6426 °2-0.0373 °2--1.3363 °2
S0.0023 Å °0.0112 Å °-0.0511 Å °-0.027 Å °-0.0205 Å °-0.0064 Å °0.086 Å °0.0048 Å °0.0189 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 235
2X-RAY DIFFRACTION1allB3 - 235
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allS1 - 564

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