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- PDB-4ynq: TREX1-dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 4ynq
TitleTREX1-dsDNA complex
Components
  • DNA (24-MER)
  • DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
  • Three-prime repair exonuclease 1
KeywordsHydrolase/DNA / protein-DNA complex / exonuclease / trex1 / 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 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
THYMIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFye, J.M. / Harvey, S. / Perrino, F.W. / Hollis, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Exonuclease TREX1 degrades double-stranded DNA to prevent spontaneous lupus-like inflammatory disease.
Authors: Grieves, J.L. / Fye, J.M. / Harvey, S. / Grayson, J.M. / Hollis, T. / Perrino, F.W.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / database_2 ...citation / database_2 / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _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 / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Revision 1.2Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
E: DNA (24-MER)
F: DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
G: DNA (24-MER)
H: DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,41113
Polymers127,9928
Non-polymers4195
Water70339
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
E: DNA (24-MER)
F: DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0446
Polymers63,9964
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-25 kcal/mol
Surface area26120 Å2
MethodPISA
2
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
G: DNA (24-MER)
H: DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3677
Polymers63,9964
Non-polymers3713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-23 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.142, 84.457, 103.000
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25693.316 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 5-235 / Mutation: D18N
Source method: isolated from a genetically manipulated source
Details: expressed as Maltose Binding Protein fusion / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami 2 (DE3) / References: UniProt: Q91XB0, exodeoxyribonuclease III

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (24-MER)


Mass: 6449.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')


Mass: 6159.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 44 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DT / THYMIDINE-5'-MONOPHOSPHATE / Thymidine monophosphate


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Comment: dTMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Feb 13, 2013 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→19.85 Å / Num. obs: 25822 / % possible obs: 94.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.102 / Χ2: 0.55 / Net I/σ(I): 5.4 / Num. measured all: 129430 / Scaling rejects: 30874
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.8-2.92.560.5331.21250531400.4446690.5
2.9-3.022.620.4651.31247331630.29417292.7
3.02-3.152.710.3591.71259932010.32392993.9
3.15-3.322.820.2782.11290332290.35379393.3
3.32-3.522.890.2362.91289832490.47350594.8
3.52-3.793.010.19641304632930.58312195.7
3.79-4.173.110.17951317433360.79281496.2
4.17-4.773.310.1127.51321633550.64210796.9
4.77-5.983.390.0998.51331633950.63179797.4
5.98-19.853.50.06614.61330034620.78117097.8

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Processing

Software
NameVersionClassification
d*TREKdata reduction
d*TREK9.9.9.1Ldata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OA8

2oa8


Resolution: 2.8→19.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2455 / WRfactor Rwork: 0.1847 / FOM work R set: 0.6843 / SU B: 20.301 / SU ML: 0.366 / SU Rfree: 0.4879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1246 4.6 %RANDOM
Rwork0.2176 ---
obs0.2198 25822 78.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.65 Å2 / Biso mean: 55.667 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å22.67 Å2
2--0.99 Å2-0 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 2.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 1686 21 39 8710
Biso mean--76.65 41.97 -
Num. residues----985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0189049
X-RAY DIFFRACTIONr_bond_other_d0.0030.027770
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.79312668
X-RAY DIFFRACTIONr_angle_other_deg1.152318000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4755897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18323.402291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.418151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9691554
X-RAY DIFFRACTIONr_chiral_restr0.0880.21366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218981
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021999
X-RAY DIFFRACTIONr_mcbond_it3.3515.4023612
X-RAY DIFFRACTIONr_mcbond_other3.3525.43611
X-RAY DIFFRACTIONr_mcangle_it5.4198.0834501
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 73 -
Rwork0.452 1613 -
all-1686 -
obs--67.06 %

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