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- PDB-5ywv: Crystal structure of TREX1 in complex with a inosine contained ssDNA -

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Basic information

Entry
Database: PDB / ID: 5ywv
TitleCrystal structure of TREX1 in complex with a inosine contained ssDNA
Components
  • INOSINE CONTAINED SSDNA
  • 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 / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 SSDNA
D: INOSINE CONTAINED SSDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,69714
Polymers60,2514
Non-polymers44610
Water3,135174
1
A: Three-prime repair exonuclease 1
C: INOSINE CONTAINED SSDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2596
Polymers30,1252
Non-polymers1344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-30 kcal/mol
Surface area11390 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
D: INOSINE CONTAINED SSDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4388
Polymers30,1252
Non-polymers3136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-55 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.192, 80.713, 85.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#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 SSDNA


Mass: 2137.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 184 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.86 Å3/Da / Density % sol: 33.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES MONOHYDRATE PH 6.0, 20%(W/V) POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 20577 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.25 / % possible all: 100

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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: 2.3→29.31 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.22 1594 7.77 %
Rwork0.159 --
obs0.164 20526 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 168 24 174 3848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063776
X-RAY DIFFRACTIONf_angle_d0.9655174
X-RAY DIFFRACTIONf_dihedral_angle_d15.9781408
X-RAY DIFFRACTIONf_chiral_restr0.038589
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.37430.27751450.18781692X-RAY DIFFRACTION100
2.3743-2.45910.2191640.17441656X-RAY DIFFRACTION100
2.4591-2.55750.25281420.181714X-RAY DIFFRACTION100
2.5575-2.67390.25561350.17021705X-RAY DIFFRACTION100
2.6739-2.81470.24021430.17991714X-RAY DIFFRACTION100
2.8147-2.99090.24691480.18071706X-RAY DIFFRACTION100
2.9909-3.22160.24011390.17981705X-RAY DIFFRACTION100
3.2216-3.54530.24391360.15791730X-RAY DIFFRACTION100
3.5453-4.05710.18821670.14441731X-RAY DIFFRACTION100
4.0571-5.10720.17471310.12661756X-RAY DIFFRACTION99
5.1072-29.30740.2071440.15371823X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -26.1873 Å / Origin y: 7.7346 Å / Origin z: -21.9613 Å
111213212223313233
T0.183 Å20.0066 Å2-0.0042 Å2-0.1337 Å2-0.0109 Å2--0.1464 Å2
L1.3632 °2-0.0208 °2-0.1489 °2-0.6738 °2-0.1683 °2--0.7219 °2
S-0.0331 Å °-0.0357 Å °-0.0215 Å °0.0086 Å °0.0496 Å °0.0271 Å °-0.0029 Å °-0.0217 Å °-0.018 Å °
Refinement TLS groupSelection details: ALL

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