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- PDB-8hce: Crystal structure of mTREX1-CMP complex -

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Basic information

Entry
Database: PDB / ID: 8hce
TitleCrystal structure of mTREX1-CMP complex
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / CMP
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
CYTIDINE-5'-MONOPHOSPHATE / AMMONIUM ION / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 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)55,5808
Polymers54,7902
Non-polymers7906
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-25 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.041, 85.655, 100.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 647 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
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: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 85211 / % possible obs: 96.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Χ2: 1.213 / Net I/σ(I): 16.9 / Num. measured all: 386279
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.20.47641840.7660.2490.5410.65795.6
1.53-1.554.20.41941910.8070.2180.4750.67896.1
1.55-1.584.20.37542010.8660.1930.4250.69996
1.58-1.624.20.32542050.90.1670.3680.72196.3
1.62-1.654.30.28642330.9260.1460.3240.74296.6
1.65-1.694.30.24342200.9450.1240.2750.78596.7
1.69-1.734.40.19842690.9650.10.2230.82796.7
1.73-1.784.50.1742780.9760.0850.1910.89897.3
1.78-1.834.50.13442920.9850.0670.1510.95197.4
1.83-1.894.50.11142540.990.0550.1251.05197.5
1.89-1.964.60.08842900.9930.0430.0981.14397.6
1.96-2.044.70.07143190.9960.0350.081.22697.9
2.04-2.134.70.05943320.9960.0290.0661.39198
2.13-2.244.70.05443250.9970.0270.0611.54597.9
2.24-2.384.70.0543380.9970.0250.0561.72897.5
2.38-2.564.80.04643110.9970.0230.0521.9697.1
2.56-2.824.80.0442810.9970.020.0451.96596.2
2.82-3.234.80.03243050.9990.0150.0361.87495.6
3.23-4.074.80.02642490.9990.0120.0291.62593.6
4.07-304.80.02241340.9990.0110.0241.19987.3

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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: 1.501→26.077 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 6626 7.78 %
Rwork0.157 78560 -
obs0.1595 85186 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.28 Å2 / Biso mean: 31.4872 Å2 / Biso min: 10.08 Å2
Refinement stepCycle: final / Resolution: 1.501→26.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 85 641 4193
Biso mean--51.63 45.36 -
Num. residues----448
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.51780.2612240.2424250194
1.5178-1.53560.23652220.231257696
1.5356-1.55430.23592090.2256261896
1.5543-1.5740.21842030.2147259496
1.574-1.59470.23072340.2092256196
1.5947-1.61660.22062000.2096261196
1.6166-1.63970.21042080.2013263496
1.6397-1.66410.24121980.1966260797
1.6641-1.69010.22832260.1907258797
1.6901-1.71780.2222210.1899261397
1.7178-1.74750.21462320.1831261197
1.7475-1.77920.21422280.1796264297
1.7792-1.81340.19972140.1701261997
1.8134-1.85040.20762150.1743262497
1.8504-1.89070.19232180.1768265398
1.8907-1.93460.21332370.168261398
1.9346-1.9830.19582160.1672266798
1.983-2.03660.19912320.1654264398
2.0366-2.09650.18082520.1569263198
2.0965-2.16410.1832340.1518264798
2.1641-2.24140.17882330.1535266698
2.2414-2.33110.19982190.1532266598
2.3311-2.43710.16442130.1449268297
2.4371-2.56550.19542220.1445264397
2.5655-2.72610.16862330.1456260796
2.7261-2.93630.18262310.1518264896
2.9363-3.23130.18811950.1521267896
3.2313-3.69780.17642440.1376257994
3.6978-4.65450.16132160.1201261193
4.6545-26.0770.20361970.1651252986
Refinement TLS params.Method: refined / Origin x: 31.9613 Å / Origin y: 0.0708 Å / Origin z: 19.1684 Å
111213212223313233
T0.0881 Å20.0073 Å20.0031 Å2-0.0898 Å20.0001 Å2--0.1227 Å2
L0.355 °20.0817 °20.0145 °2-0.6387 °2-0.0242 °2--1.1699 °2
S0.0052 Å °0.0064 Å °-0.0358 Å °-0.021 Å °-0.0219 Å °-0.0025 Å °0.0671 Å °0.0177 Å °0.0191 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 DIFFRACTION1allD2
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allS1 - 641

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