[English] 日本語
Yorodumi
- PDB-5ywt: Crystal structure of TREX1 in complex with a duplex DNA with 3' o... -

+
Open data


ID or keywords:

Loading...

-
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


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 / oligosaccharyltransferase complex / DNA exonuclease activity / DNA modification / regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / regulation of protein complex stability / heart process / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / regulation of lysosome organization / 3'-5'-DNA exonuclease activity / regulation of cellular respiration / MutLalpha complex binding / regulation of tumor necrosis factor production / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / DNA catabolic process / regulation of immunoglobulin production / regulation of T cell activation / apoptotic cell clearance / DNA binding, bending / regulation of glycolytic process / regulation of metabolic process / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / regulation of innate immune response / WW domain binding / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated 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 / cellular response to reactive oxygen species / generation of precursor metabolites and energy / kidney development / establishment of protein localization / cellular response to gamma radiation / protein-DNA complex / 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: 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
Revision 1.2Jul 17, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

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)71,55511
Polymers71,2814
Non-polymers2747
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4620 Å2
ΔGint-85 kcal/mol
Surface area21720 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

-
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


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more