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- PDB-5ywu: Crystal structure of TREX1 in complex with a inosine contained dsDNA -

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Basic information

Entry
Database: PDB / ID: 5ywu
TitleCrystal structure of TREX1 in complex with a inosine contained dsDNA
Components
  • INOSINE CONTAINED DSDNAS
  • Three-prime repair exonuclease 1
KeywordsDNA BINDING PROTEIN/DNA / exonuclease / DEDDh family / protein-DNA complex / DNA BINDING PROTEIN-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 / WW domain binding / heart process / MutLalpha complex binding / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 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 / 3'-5'-DNA exonuclease activity / regulation of T cell activation / regulation of glycolytic process / DNA binding, bending / DNA duplex unwinding / negative regulation of type I interferon-mediated signaling pathway / cellular response to organic substance / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / regulation of innate immune response / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / 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 / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHsiao, Y.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST103-2311-B-009-001-MY3 Taiwan
CitationJournal: PLoS Biol. / Year: 2018
Title: Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1
Authors: Huang, K.W. / Liu, T.C. / Liang, R.Y. / Chu, L.Y. / Cheng, H.L. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionNov 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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: INOSINE CONTAINED DSDNAS
D: INOSINE CONTAINED DSDNAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1588
Polymers70,0614
Non-polymers974
Water0
1
A: Three-prime repair exonuclease 1
C: INOSINE CONTAINED DSDNAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0794
Polymers35,0302
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-28 kcal/mol
Surface area12470 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
D: INOSINE CONTAINED DSDNAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0794
Polymers35,0302
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-28 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.180, 133.180, 76.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 27987.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: DNA chain INOSINE CONTAINED DSDNAS


Mass: 7042.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M POTASSIUM CITRATE TRIBASIC MONOHYDRATE, PH 8.3, 20%(W/V) POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. obs: 9877 / % possible obs: 99.5 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24.6
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXM

3mxm


Resolution: 3.4→29.78 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 29.71
RfactorNum. reflection% reflection
Rfree0.254 746 7.59 %
Rwork0.223 --
obs0.225 9824 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 534 4 0 4053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034198
X-RAY DIFFRACTIONf_angle_d0.5825820
X-RAY DIFFRACTIONf_dihedral_angle_d18.0461585
X-RAY DIFFRACTIONf_chiral_restr0.024665
X-RAY DIFFRACTIONf_plane_restr0.003668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.66210.37521450.34351765X-RAY DIFFRACTION99
3.6621-4.02980.31761460.27261763X-RAY DIFFRACTION99
4.0298-4.61110.22921510.19961785X-RAY DIFFRACTION100
4.6111-5.80250.22921540.22021825X-RAY DIFFRACTION100
5.8025-29.78110.22841500.19291940X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -42.3381 Å / Origin y: 14.5789 Å / Origin z: 10.432 Å
111213212223313233
T0.8953 Å2-0.1047 Å20.0887 Å2-0.8403 Å2-0.0692 Å2--0.668 Å2
L2.3252 °20.1079 °21.0175 °2-2.479 °20.0793 °2--2.3529 °2
S0.0993 Å °0.1137 Å °-0.1742 Å °0.0985 Å °-0.0404 Å °0.0814 Å °-0.0959 Å °-0.0719 Å °-0.0753 Å °
Refinement TLS groupSelection details: ALL

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