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- PDB-5ywt: Crystal structure of TREX1 in complex with a duplex DNA with 3' o... -

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Basic information

Entry
Database: PDB / ID: 5ywt
TitleCrystal structure of TREX1 in complex with a duplex DNA with 3' overhang
Components
  • DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
  • Three-prime repair exonuclease 1
KeywordsDNA BINDING PROTEIN / TREX1 / 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 / 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: 1.7 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.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
D: DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
C: DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,55511
Polymers71,2814
Non-polymers2747
Water10,233568
1
A: Three-prime repair exonuclease 1
C: DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8076
Polymers35,6412
Non-polymers1664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-45 kcal/mol
Surface area11600 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
D: DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7485
Polymers35,6412
Non-polymers1083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-37 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.170, 80.350, 85.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29876.902 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 DNA (5'-D(*GP*GP*CP*CP*CP*T)-3')


Mass: 5763.708 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
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 1.59 Å3/Da / Density % sol: 22.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M BICINE PH 8.5, 20%(W/V) POLYETHYLENE GLYCOL 10,000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 50099 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.3 / % possible all: 96.6

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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: 1.7→28.79 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 21.42
RfactorNum. reflection% reflection
Rfree0.219 2513 5.06 %
Rwork0.194 --
obs0.196 49630 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 295 7 568 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033839
X-RAY DIFFRACTIONf_angle_d0.8715291
X-RAY DIFFRACTIONf_dihedral_angle_d16.7511457
X-RAY DIFFRACTIONf_chiral_restr0.031606
X-RAY DIFFRACTIONf_plane_restr0.004639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73270.3411300.31782520X-RAY DIFFRACTION97
1.7327-1.76810.33471420.29322554X-RAY DIFFRACTION96
1.7681-1.80650.3261260.29222547X-RAY DIFFRACTION97
1.8065-1.84850.29751240.26482584X-RAY DIFFRACTION97
1.8485-1.89480.27161360.24442592X-RAY DIFFRACTION97
1.8948-1.9460.28821410.23442556X-RAY DIFFRACTION97
1.946-2.00320.20881320.21092589X-RAY DIFFRACTION98
2.0032-2.06790.2271510.19312569X-RAY DIFFRACTION98
2.0679-2.14170.19891230.18082598X-RAY DIFFRACTION98
2.1417-2.22750.1991430.18122598X-RAY DIFFRACTION98
2.2275-2.32880.19861340.18262598X-RAY DIFFRACTION98
2.3288-2.45150.23741420.18732671X-RAY DIFFRACTION99
2.4515-2.6050.22351540.19152595X-RAY DIFFRACTION99
2.605-2.8060.20171460.18612660X-RAY DIFFRACTION99
2.806-3.08810.21861410.18462663X-RAY DIFFRACTION99
3.0881-3.53420.17691530.17182670X-RAY DIFFRACTION99
3.5342-4.45010.17241380.14922727X-RAY DIFFRACTION99
4.4501-28.7980.22111570.18742826X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -7.3623 Å / Origin y: -7.6745 Å / Origin z: 19.979 Å
111213212223313233
T0.1033 Å20.0074 Å20.0229 Å2-0.0604 Å2-0.0022 Å2--0.0734 Å2
L1.2527 °20.0596 °20.2619 °2-0.9751 °20.1262 °2--0.8808 °2
S0.0134 Å °-0.0277 Å °-0.0124 Å °-0.0277 Å °0.0194 Å °-0.0149 Å °-0.0169 Å °-0.0225 Å °-0.0238 Å °
Refinement TLS groupSelection details: ALL

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