[English] 日本語
Yorodumi
- PDB-8hch: Crystal structure of mTREX1-Uridine complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hch
TitleCrystal structure of mTREX1-Uridine complex
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / Uridine
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 / WW domain binding / regulation of innate immune response / 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 / 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 / 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 superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
URIDINE / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHsiao, Y.Y. / Huang, K.W. / Wu, C.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 111-2636-B-A49-006 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids.
Authors: Huang, K.W. / Wu, C.Y. / Toh, S.I. / Liu, T.C. / Tu, C.I. / Lin, Y.H. / Cheng, A.J. / Kao, Y.T. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionNov 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,86312
Polymers109,7894
Non-polymers1,0748
Water8,251458
1
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4316
Polymers54,8942
Non-polymers5374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-16 kcal/mol
Surface area18000 Å2
2
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4316
Polymers54,8942
Non-polymers5374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-16 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.632, 81.149, 93.653
Angle α, β, γ (deg.)90.000, 103.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 27447.154 Da / Num. of mol.: 4
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.2% w/v Cytidine, 0.2% w/v Inosine, 0.2% w/v Ribavirin, 0.2% w/v Thymidine, 0.2% w/v Uridine, 0.1M Imidazole, 0.1M MES monohydrate (acid), pH6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 66457 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Χ2: 1.448 / Net I/σ(I): 12.4 / Num. measured all: 285244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.49532830.7250.280.5720.69299.6
2.03-2.073.80.45332860.8170.2650.5280.91299.3
2.07-2.113.80.39233040.7930.2250.4540.83899.3
2.11-2.1540.31932690.8820.1770.3660.78599.7
2.15-2.24.10.29133460.9020.1610.3340.82499.5
2.2-2.253.80.29233360.8770.1680.3381.13899.4
2.25-2.314.10.23332420.930.1280.2681.04399.3
2.31-2.374.40.18933360.9670.10.2140.946100
2.37-2.444.40.17233230.9720.0910.1951.00399.9
2.44-2.524.50.14433500.9790.0760.1631.09199.9
2.52-2.614.50.1233370.9850.0630.1361.19599.9
2.61-2.714.50.11133330.9850.0590.1261.44399.9
2.71-2.844.50.08933290.9920.0460.11.42999.9
2.84-2.994.60.07433090.9940.0380.0841.58699.9
2.99-3.174.60.0633410.9960.0310.0681.89199.8
3.17-3.424.60.0533430.9980.0260.0571.9899.7
3.42-3.764.50.04533420.9980.0230.0512.2999.4
3.76-4.314.60.0433160.9980.0210.0462.26899.5
4.31-5.424.50.0433680.9970.0210.0462.41699.5
5.42-304.10.03833640.9970.0220.0442.55297.6

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YWS

5yws


Resolution: 2→24.69 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 5114 7.72 %
Rwork0.187 61161 -
obs0.1901 66275 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.55 Å2 / Biso mean: 46.4932 Å2 / Biso min: 18.58 Å2
Refinement stepCycle: final / Resolution: 2→24.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 140 438 7335
Biso mean--45.56 45.58 -
Num. residues----873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.28381820.255619992181100
2.02-2.050.2791730.254720402213100
2.05-2.070.30881680.25292005217399
2.07-2.10.2811830.24332001218499
2.1-2.130.25061560.232120582214100
2.13-2.150.26211830.212219912174100
2.15-2.190.25461700.216520422212100
2.19-2.220.25681710.221520282199100
2.22-2.250.26021840.23062045222999
2.25-2.290.25071690.21051998216799
2.29-2.330.25991680.208420342202100
2.33-2.370.2521580.199820512209100
2.37-2.420.22151500.212220552205100
2.42-2.470.23931700.204220342204100
2.47-2.520.27571770.200920492226100
2.52-2.580.24971740.197820342208100
2.58-2.640.23331530.187220552208100
2.64-2.710.25881750.200320502225100
2.71-2.790.23491550.209220562211100
2.79-2.880.25941580.197820402198100
2.88-2.990.23551650.203620502215100
2.99-3.110.22032130.189420252238100
3.11-3.250.25881520.199120552207100
3.25-3.420.22811760.185620392215100
3.42-3.630.24791710.17882032220399
3.63-3.910.18231710.164520702241100
3.91-4.30.19151880.149920062194100
4.3-4.920.1761570.139120842241100
4.92-6.180.19861760.17562074225099
6.18-24.690.22451680.18292061222997
Refinement TLS params.Method: refined / Origin x: 35.4128 Å / Origin y: -16.9027 Å / Origin z: 24.6255 Å
111213212223313233
T0.2201 Å2-0.0067 Å20.0016 Å2-0.2107 Å20.0379 Å2--0.2206 Å2
L0.1123 °2-0.0871 °2-0.0507 °2-0.5799 °20.4761 °2--0.3433 °2
S-0.0392 Å °0.0035 Å °0.0043 Å °-0.0538 Å °0.0326 Å °0.0374 Å °-0.0394 Å °0.0071 Å °0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 234
2X-RAY DIFFRACTION1allB10 - 234
3X-RAY DIFFRACTION1allC10 - 234
4X-RAY DIFFRACTION1allD10 - 234
5X-RAY DIFFRACTION1allF1 - 4
6X-RAY DIFFRACTION1allS1 - 438
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1

+
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