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- PDB-5yws: Crystal structure of TREX1 in complex with a Y structured DNA -

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Basic information

Entry
Database: PDB / ID: 5yws
TitleCrystal structure of TREX1 in complex with a Y structured DNA
Components
  • A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL
  • Three-prime repair exonuclease 1
KeywordsDNA BINDING PROTEIN/DNA / DEDDh / Exouclease / Protein-DNA complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / organ or tissue specific immune response / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation / MutSalpha complex binding ...cellular response to type I interferon / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / immune complex formation / organ or tissue specific immune response / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / DNA exonuclease activity / DNA modification / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / lymphoid progenitor cell differentiation / regulation of type I interferon production / cellular response to hydroxyurea / regulation of lysosome organization / 3'-5'-DNA exonuclease activity / regulation of cellular respiration / regulation of tumor necrosis factor production / MutLalpha complex binding / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / regulation of immunoglobulin production / regulation of metabolic process / DNA catabolic process / regulation of T cell activation / apoptotic cell clearance / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / DNA binding, bending / WW domain binding / type I interferon-mediated signaling pathway / DNA metabolic process / regulation of innate immune response / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / heart morphogenesis / response to UV / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / determination of adult lifespan / generation of precursor metabolites and energy / cellular response to reactive oxygen species / kidney development / establishment of protein localization / protein-DNA complex / cellular response to gamma radiation / cellular response to UV / single-stranded DNA binding / regulation of gene expression / regulation of inflammatory response / cellular response to oxidative stress / double-stranded DNA binding / defense response to virus / adaptive immune response / DNA replication / 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 / cytoplasm / cytosol
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: 2 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: A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL
D: A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2728
Polymers73,1744
Non-polymers974
Water7,440413
1
A: Three-prime repair exonuclease 1
C: A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6364
Polymers36,5872
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-32 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
D: A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6364
Polymers36,5872
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-28 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.532, 96.604, 101.112
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 A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL


Mass: 6710.313 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5, 30%(V/V) POLYETHYLENE GLYCOL 300, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 4.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→29.33 Å / Num. obs: 39153 / % possible obs: 97.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

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

3mxm


Resolution: 2→29.33 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.226 3005 7.71 %
Rwork0.189 --
obs0.192 38969 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 748 4 413 4734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044490
X-RAY DIFFRACTIONf_angle_d0.8516266
X-RAY DIFFRACTIONf_dihedral_angle_d18.7631723
X-RAY DIFFRACTIONf_chiral_restr0.032714
X-RAY DIFFRACTIONf_plane_restr0.003691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.28491560.23061661X-RAY DIFFRACTION97
2.0328-2.06780.26231570.22271733X-RAY DIFFRACTION100
2.0678-2.10540.25871230.21851771X-RAY DIFFRACTION100
2.1054-2.14590.25831380.20751733X-RAY DIFFRACTION100
2.1459-2.18970.23011600.20581719X-RAY DIFFRACTION100
2.1897-2.23730.26731240.23261404X-RAY DIFFRACTION81
2.2373-2.28930.4491950.35721263X-RAY DIFFRACTION71
2.2893-2.34660.2591440.21191722X-RAY DIFFRACTION100
2.3466-2.410.21721350.20111775X-RAY DIFFRACTION100
2.41-2.48080.21991350.19621760X-RAY DIFFRACTION100
2.4808-2.56090.22911140.18971756X-RAY DIFFRACTION100
2.5609-2.65230.21641720.19891731X-RAY DIFFRACTION100
2.6523-2.75850.26321430.20211759X-RAY DIFFRACTION100
2.7585-2.88390.25421330.20421769X-RAY DIFFRACTION100
2.8839-3.03580.26171480.20711769X-RAY DIFFRACTION100
3.0358-3.22580.23731580.20751755X-RAY DIFFRACTION100
3.2258-3.47450.21221370.18531795X-RAY DIFFRACTION100
3.4745-3.82350.19791590.16721706X-RAY DIFFRACTION97
3.8235-4.37520.18591440.14881815X-RAY DIFFRACTION100
4.3752-5.50630.17961810.14581780X-RAY DIFFRACTION100
5.5063-29.33290.22771490.17461788X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -21.7487 Å / Origin y: 15.3406 Å / Origin z: -11.9242 Å
111213212223313233
T0.1633 Å20.0254 Å2-0.0044 Å2-0.1805 Å2-0.0206 Å2--0.1751 Å2
L0.7328 °20.2067 °20.0612 °2-1.0824 °2-0.2492 °2--0.8809 °2
S-0.0021 Å °-0.0297 Å °-0.0244 Å °-0.0242 Å °-0.0166 Å °-0.026 Å °0.0779 Å °0.0169 Å °0.012 Å °
Refinement TLS groupSelection details: ALL

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