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- PDB-2o4i: Structure of TREX1 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 2o4i
TitleStructure of TREX1 in complex with DNA
Components
  • 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / TREX1 / exonuclease / DnaQ / DNA complex / WW motif / protein-protein interaction / polyproline binding motif / 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 type I interferon production / regulation of protein complex stability / cellular response to hydroxyurea / 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 / regulation of immunoglobulin production / DNA catabolic process / apoptotic cell clearance / regulation of T cell activation / DNA binding, bending / DNA duplex unwinding / regulation of glycolytic process / DNA metabolic process / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / regulation of innate immune response / 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 / kidney development / generation of precursor metabolites and energy / 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 / DNA (> 10) / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBrucet, M. / Macias, M.J. / Fita, I. / Celada, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains.
Authors: Brucet, M. / Querol-Audi, J. / Serra, M. / Ramirez-Espain, X. / Bertlik, K. / Ruiz, L. / Lloberas, J. / Macias, M.J. / Fita, I. / Celada, A.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3'
D: 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3'
A: Three prime repair exonuclease 1
B: Three prime repair exonuclease 1


Theoretical massNumber of molelcules
Total (without water)69,2944
Polymers69,2944
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.758, 80.758, 171.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY3AC9 - 23411 - 236
21GLYGLYGLYGLY3BD9 - 23411 - 236
12DCDCDTDT1CA1001 - 100422 - 25
22DCDCDTDT1DB1001 - 100422 - 25

NCS ensembles :
ID
1
2

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Components

#1: DNA chain 5'-D(*GP*CP*TP*AP*GP*GP*CP*AP*GP*GP*AP*AP*CP*CP*CP*CP*TP*CP*CP*TP*CP*CP*CP*CP*T)-3'


Mass: 7540.849 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Three prime repair exonuclease 1 / 3'-5' exonuclease TREX1


Mass: 27105.941 Da / Num. of mol.: 2 / Fragment: TREX1 exonuclease / Mutation: H195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Plasmid: pETM-10 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q91XB0, exodeoxyribonuclease III

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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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 2KMME, 0.1M Imidazole, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2KMME11
2Imidazole11
3lithium sulfate11
4H2O11
5PEG 2KMME12
6lithium sulfate12
7H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.5→25 Å / Num. all: 6708 / Num. obs: 6708 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.156 / Net I/σ(I): 3.7
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.44 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O4G

2o4g


Resolution: 3.5→24.85 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.871 / SU B: 101.221 / SU ML: 0.671 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.779 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28335 321 4.6 %RANDOM
Rwork0.24333 ---
all0.24516 6402 --
obs0.24516 6402 87.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.203 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å20 Å20 Å2
2---3.41 Å20 Å2
3---6.82 Å2
Refinement stepCycle: LAST / Resolution: 3.5→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 154 0 0 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223611
X-RAY DIFFRACTIONr_bond_other_d0.0010.022441
X-RAY DIFFRACTIONr_angle_refined_deg1.0072.0414948
X-RAY DIFFRACTIONr_angle_other_deg0.76735976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5095432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81423.475141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42615564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3371527
X-RAY DIFFRACTIONr_chiral_restr0.050.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_nbd_refined0.1630.2795
X-RAY DIFFRACTIONr_nbd_other0.1520.22429
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21749
X-RAY DIFFRACTIONr_nbtor_other0.080.21828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0351.52837
X-RAY DIFFRACTIONr_mcbond_other0.011.5856
X-RAY DIFFRACTIONr_mcangle_it0.04423542
X-RAY DIFFRACTIONr_scbond_it0.08531638
X-RAY DIFFRACTIONr_scangle_it0.134.51406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1270tight positional0.010.05
2C114tight positional0.120.05
1A1579loose positional0.435
1A1270tight thermal0.010.5
2C114tight thermal0.010.5
1A1579loose thermal0.0710
LS refinement shellResolution: 3.5→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 16 -
Rwork0.296 321 -
obs--63.11 %
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)
15.5884-0.8910.46546.5923-1.10084.73980.14460.22820.6323-0.284-0.2999-0.2276-0.2401-0.15680.1553-0.7797-0.07350.123-0.11370.234-0.314915.648726.84221.5918
27.11920.72730.41765.9671-0.91374.32650.02480.2255-0.632-0.27720.1290.03150.570.2285-0.1538-0.70190.0970.0173-0.19390.1783-0.489714.13340.290625.2059
320.299122.4164-28.126225.1112-32.790647.37050.2014-1.41590.58284.18682.07444.2002-6.0252-2.2784-2.27580.01020.09550.25460.32430.35980.28868.321637.766427.7552
456.538235.4401-20.522895.5164-27.551438.1379-0.98461.3823-3.1185-3.30061.0252-1.87954.3788-1.4526-0.0406-0.26070.1177-0.07010.23970.1025-0.15269.6867-10.25416.2714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC9 - 23411 - 236
2X-RAY DIFFRACTION2BD9 - 23411 - 236
3X-RAY DIFFRACTION3CA1001 - 100422 - 25
4X-RAY DIFFRACTION4DB1001 - 100422 - 25

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