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- PDB-2oa8: Crystal Structure of mTREX1 with ssDNA -

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Basic information

Entry
Database: PDB / ID: 2oa8
TitleCrystal Structure of mTREX1 with ssDNA
Components
  • 5'-D(*GP*AP*CP*G)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / poly-proline helix / ssDNA complex / DnaQ family / HYDROLASE-DNA COMPLEX
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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Silva, U. / Hollis, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals a Polyproline II Helix for Protein Partnering.
Authors: de Silva, U. / Choudhury, S. / Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*AP*CP*G)-3'
D: 5'-D(*GP*AP*CP*G)-3'
A: Three prime repair exonuclease 1
B: Three prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7608
Polymers53,5994
Non-polymers1604
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.850, 57.141, 68.470
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is the dimer in the asymmetric unit

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Components

#1: DNA chain 5'-D(*GP*AP*CP*G)-3'


Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1


Mass: 25583.844 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 5-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q91XB0, exodeoxyribonuclease III
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 3350, 50mM MES, pH 6.5, 50mM HEPES, pH 7.15, 2mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2MES11
3HEPES11
4CaCl211
5HOH11
6PEG 335012
7MES12
8HEPES12
9CaCl212
10HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 21, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→61.86 Å / Num. all: 37899 / Num. obs: 37899 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 3.51 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 2.11→2.22 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3936 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IOC

2ioc


Resolution: 2.1→61.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.956 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25916 1401 5 %RANDOM
Rwork0.1919 ---
obs0.19514 26646 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.719 Å2
Baniso -1Baniso -2Baniso -3
1--3.35 Å20 Å2-1.13 Å2
2--3.46 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3437 162 4 288 3891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9522.0435085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2415441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81823.472144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76415568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9681526
X-RAY DIFFRACTIONr_chiral_restr0.1370.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21849
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2670.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.52316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54323629
X-RAY DIFFRACTIONr_scbond_it2.42931650
X-RAY DIFFRACTIONr_scangle_it3.5134.51456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 105 -
Rwork0.237 1971 -
obs-3956 99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0142-0.09960.88642.8194-0.01661.7134-0.00140.376-0.34640.3037-0.0149-0.00530.1186-0.08120.0163-0.0931-0.02690.05340.0036-0.0419-0.07534.32916.9914-19.3446
22.1187-0.60470.41631.28-0.19261.22680.04680.3287-0.14120.0525-0.0860.1929-0.1005-0.08020.0392-0.1356-0.021-0.0053-0.0049-0.04-0.13575.212912.8508-20.5916
32.343-0.15820.45031.9792-0.21642.0972-0.0479-0.0947-0.37250.2656-0.03160.20040.1615-0.30410.0795-0.1028-0.0180.0604-0.1187-0.0241-0.05310.77696.7921-11.4859
44.0077-1.20420.64921.5046-0.22441.37510.12680.49630.4106-0.1295-0.1804-0.31710.00740.130.0536-0.1546-0.0090.0149-0.02440.0799-0.12328.237715.1791-20.6503
53.5103-0.555-0.55653.2134-0.19363.6144-0.04870.44290.69960.2139-0.0529-0.6055-0.00690.34910.1016-0.1476-0.0285-0.1101-0.15110.06430.119633.007220.2555-13.4964
69.65166.7501-2.288819.20355.5794.1022-0.2401-0.2376-0.02340.02370.3845-1.45190.04060.2128-0.1443-0.0928-0.0412-0.15480.12860.06940.179641.249810.1894-12.1539
710.202710.0537-7.088120.2123-8.61545.1824-0.35270.19890.1477-0.15610.17130.81710.1027-0.21840.1814-0.0439-0.04370.04730.09450.005-0.009-7.500417.4522-11.9033
8106.6243-118.559-17.2212326.813-166.0495254.3536-0.18692.9364-0.7892-2.49821.31640.1773-4.26136.4672-1.1295-0.07260.0999-0.06930.00510.00890.00831.761710.9028-13.7392
9139.449-108.0311-11.28790.1279-1.989218.8129-3.013-3.3511-4.27974.4835-3.6114-1.69845.4776.19786.6244-0.0127-0.0110.1563-0.0160.19240.12251.750616.8314-13.5082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 47
2X-RAY DIFFRACTION2A51 - 166
3X-RAY DIFFRACTION3A175 - 235
4X-RAY DIFFRACTION4B4 - 166
5X-RAY DIFFRACTION5B174 - 236
6X-RAY DIFFRACTION6C1 - 4
7X-RAY DIFFRACTION7D1 - 4
8X-RAY DIFFRACTION8B301
9X-RAY DIFFRACTION8C302
10X-RAY DIFFRACTION9D401
11X-RAY DIFFRACTION9A402

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