[English] 日本語
Yorodumi
- PDB-9kjm: The mTREX1-NSC 37204 complex structure by soaking in Soaking Cond... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kjm
TitleThe mTREX1-NSC 37204 complex structure by soaking in Soaking Condition 1 (NSC 37204 complex 3)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / Inhibitor / DEDDh exonuclease
Function / homology
Function and homology information


immune response in brain or nervous system / immune complex formation / T cell antigen processing and presentation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition ...immune response in brain or nervous system / immune complex formation / T cell antigen processing and presentation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition / MutSalpha complex binding / regulation of catalytic activity / DNA exonuclease activity / DNA modification / regulation of immunoglobulin production / cellular response to hydroxyurea / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of cellular respiration / regulation of fatty acid metabolic process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / inflammatory response to antigenic stimulus / regulation of tumor necrosis factor production / heart process / regulation of T cell activation / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / glycoprotein biosynthetic process / DNA catabolic process / apoptotic cell clearance / negative regulation of type I interferon-mediated signaling pathway / regulation of glycolytic process / DNA binding, bending / blood vessel development / cellular response to type I interferon / type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / WW domain binding / regulation of innate immune response / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / nuclear replication fork / heart morphogenesis / response to UV / cellular response to interferon-beta / determination of adult lifespan / kidney development / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / DNA damage checkpoint signaling / negative regulation of innate immune response / generation of precursor metabolites and energy / establishment of protein localization / cellular response to reactive oxygen species / cellular response to gamma radiation / protein-DNA complex / cellular response to UV / single-stranded DNA binding / regulation of gene expression / cellular response to oxidative stress / regulation of inflammatory response / 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 / 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 superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / ACETATE ION / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHsiao, Y.Y. / Huang, K.W. / Wu, C.Y. / Tsai, C.Y. / Wu, M.T.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)NSTC 112-2636-B-A49-004 - Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC 112-2628-B-A49 -008 -MY3 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Disordered DNA-binding motif forms a modulation site for inhibiting the cancer immunotherapy target TREX1.
Authors: Huang, K.W. / Yu Tsai, C. / Wu, C.Y. / Lin, W.C. / Wu, M.T. / Hsu, K.C. / Yu Yang, C. / Chang, I.Y. / Liu, H.M. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7539
Polymers54,8942
Non-polymers8597
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint1 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.752, 83.015, 88.610
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


Mass: 27447.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-A1L5Z / 4-oxidanyl-6-[(8-oxidanyl-6-sulfo-naphthalen-2-yl)carbamoylamino]naphthalene-2-sulfonic acid / NSC-37204


Mass: 504.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N2O9S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium cacodylate trihydrate pH 6.5, 1.4M Sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 61686 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Χ2: 2.093 / Net I/σ(I): 13.3 / Num. measured all: 387571
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.766.80.42460880.9170.9780.1750.460.814100
1.76-1.836.50.3160950.9520.9880.1310.3371.007100
1.83-1.917.10.2560780.9710.9930.1020.271.367100
1.91-2.026.40.17661240.9850.9960.0760.1921.58699.9
2.02-2.146.80.12861100.9910.9980.0540.1391.91599.9
2.14-2.316.60.10961500.9930.9980.0470.1192.46499.8
2.31-2.546.40.0861760.9950.9990.0350.0882.61299.9
2.54-2.915.90.06761790.9950.9990.0310.0743.12799.9
2.91-3.665.10.05462230.9960.9990.0260.063.4999.5
3.66-305.40.04664630.9970.9990.0220.0513.34999.4

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTV4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→23.66 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 4807 7.8 %
Rwork0.1565 --
obs0.159 61594 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 58 500 4030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113679
X-RAY DIFFRACTIONf_angle_d1.1875031
X-RAY DIFFRACTIONf_dihedral_angle_d6.342506
X-RAY DIFFRACTIONf_chiral_restr0.063567
X-RAY DIFFRACTIONf_plane_restr0.016659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.27421440.21271690X-RAY DIFFRACTION90
1.72-1.740.26521690.21631867X-RAY DIFFRACTION100
1.74-1.760.25931690.20791897X-RAY DIFFRACTION100
1.76-1.780.22781570.19171836X-RAY DIFFRACTION100
1.78-1.810.19831600.18131915X-RAY DIFFRACTION100
1.81-1.830.18661620.17441856X-RAY DIFFRACTION100
1.83-1.860.21851610.17861861X-RAY DIFFRACTION100
1.86-1.890.2021790.17641882X-RAY DIFFRACTION100
1.89-1.920.21711440.18321856X-RAY DIFFRACTION100
1.92-1.950.22451430.16941907X-RAY DIFFRACTION100
1.95-1.980.20561620.16541905X-RAY DIFFRACTION100
1.98-2.020.19061440.16581893X-RAY DIFFRACTION100
2.02-2.060.1751490.16171870X-RAY DIFFRACTION100
2.06-2.10.18161430.16141907X-RAY DIFFRACTION100
2.1-2.140.17021540.14681887X-RAY DIFFRACTION100
2.14-2.190.1841570.1491881X-RAY DIFFRACTION100
2.19-2.250.191320.1621944X-RAY DIFFRACTION100
2.25-2.310.18951820.14791867X-RAY DIFFRACTION100
2.31-2.380.19411720.15211880X-RAY DIFFRACTION100
2.38-2.450.19321870.15031856X-RAY DIFFRACTION100
2.45-2.540.16831880.14431891X-RAY DIFFRACTION100
2.54-2.640.17411560.14811890X-RAY DIFFRACTION100
2.64-2.760.20921440.16121931X-RAY DIFFRACTION100
2.76-2.910.18161690.15561901X-RAY DIFFRACTION100
2.91-3.090.18631460.16141926X-RAY DIFFRACTION100
3.09-3.330.21751700.15331928X-RAY DIFFRACTION100
3.33-3.660.19281690.15611900X-RAY DIFFRACTION99
3.66-4.190.17451800.13431928X-RAY DIFFRACTION100
4.19-5.270.13131360.13131994X-RAY DIFFRACTION100
5.27-23.660.2021790.18062041X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.9577 Å / Origin y: -7.9829 Å / Origin z: -20.0054 Å
111213212223313233
T0.1306 Å20.0111 Å2-0.0075 Å2-0.1534 Å20.0097 Å2--0.1406 Å2
L0.4588 °2-0.0198 °2-0.1386 °2-0.896 °20.1012 °2--0.5756 °2
S0.0077 Å °0.0259 Å °0.0037 Å °-0.0006 Å °-0.0273 Å °0.0632 Å °0.0193 Å °-0.0216 Å °0 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