[English] 日本語
Yorodumi
- PDB-8hcc: Crystal structure of mTREX1-RNA product complex (AMP) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hcc
TitleCrystal structure of mTREX1-RNA product complex (AMP)
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / TREX1 / DEDDh exonuclease / DNase / RNase / AMP
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 ...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 / heart process / regulation of fatty acid metabolic process / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 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 / macrophage activation involved in immune response / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of metabolic process / DNA binding, bending / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / type I interferon-mediated signaling pathway / WW domain binding / DNA metabolic process / regulation of innate immune response / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / response to UV / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / kidney development / generation of precursor metabolites and energy / determination of adult lifespan / cellular response to reactive oxygen species / 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 / double-stranded DNA binding / regulation of inflammatory response / 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 / 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
ADENOSINE MONOPHOSPHATE / 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)121,20621
Polymers119,5084
Non-polymers1,69817
Water11,674648
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,61411
Polymers59,7542
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-84 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: Three-prime repair exonuclease 1
D: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,59110
Polymers59,7542
Non-polymers8388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-73 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.197, 86.433, 75.218
Angle α, β, γ (deg.)90.000, 97.600, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 29876.902 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 22, 2015
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: 61417 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.042 / Rrim(I) all: 0.085 / Χ2: 1.71 / Net I/σ(I): 12.2 / Num. measured all: 252782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0740.47760880.7970.2730.5511.35899.9
2.07-2.1540.34761590.8840.1980.41.40999.9
2.15-2.254.10.2861000.9190.1590.3231.439100
2.25-2.374.10.21260960.9560.120.2441.43299.9
2.37-2.524.10.16461160.9750.0920.1891.47699.9
2.52-2.714.20.12361370.9850.0690.1411.61399.8
2.71-2.994.20.08761490.9930.0480.11.73199.9
2.99-3.424.20.05761620.9960.0310.0651.999.9
3.42-4.314.10.04761510.9970.0260.0542.486100
4.31-304.10.03962590.9970.0220.0452.21299.7

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YWS

5yws


Resolution: 2→27.164 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2102 4759 7.8 %
Rwork0.1667 56225 -
obs0.1701 60984 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.18 Å2 / Biso mean: 36.1577 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2→27.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 153 648 7802
Biso mean--38.66 37.38 -
Num. residues----907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.28071710.22891824100
2.0227-2.04650.27321660.22561859100
2.0465-2.07150.24691630.21041881100
2.0715-2.09770.23851640.20321865100
2.0977-2.12530.22641640.19911837100
2.1253-2.15440.22951310.19491922100
2.1544-2.18510.22831360.18951842100
2.1851-2.21770.23691650.20031897100
2.2177-2.25240.24421590.19191864100
2.2524-2.28930.23791510.17691887100
2.2893-2.32870.23331530.17751846100
2.3287-2.37110.20711750.17621855100
2.3711-2.41660.23061340.17141895100
2.4166-2.46590.22421630.17531858100
2.4659-2.51950.23671440.17191880100
2.5195-2.57810.21851420.16761861100
2.5781-2.64250.22171700.16831900100
2.6425-2.71390.21811520.17891861100
2.7139-2.79370.22881720.17221880100
2.7937-2.88370.21041770.17671842100
2.8837-2.98670.2111290.17221906100
2.9867-3.10610.21951680.17231882100
3.1061-3.24730.23941530.17431870100
3.2473-3.41810.20411610.16611880100
3.4181-3.63180.18271560.15541867100
3.6318-3.91150.19241690.14951885100
3.9115-4.30370.17081720.13251865100
4.3037-4.92330.18951610.12631894100
4.9233-6.19070.21331810.16011891100
6.1907-27.1640.18131570.1676192999
Refinement TLS params.Method: refined / Origin x: 12.3214 Å / Origin y: 1.0209 Å / Origin z: 29.5066 Å
111213212223313233
T0.2049 Å20.0031 Å20.0211 Å2-0.2068 Å2-0.0023 Å2--0.2331 Å2
L0.222 °20.0109 °20.2627 °2-0.0322 °20.0747 °2--0.4413 °2
S-0.0122 Å °-0.0567 Å °-0.0005 Å °-0.0016 Å °0.0179 Å °-0.0175 Å °-0.0374 Å °0.0042 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 234
2X-RAY DIFFRACTION1allB5 - 234
3X-RAY DIFFRACTION1allC5 - 235
4X-RAY DIFFRACTION1allD5 - 234
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allJ1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allL1
13X-RAY DIFFRACTION1allM1
14X-RAY DIFFRACTION1allN1
15X-RAY DIFFRACTION1allO1
16X-RAY DIFFRACTION1allP1
17X-RAY DIFFRACTION1allS1 - 649
18X-RAY DIFFRACTION1allQ1
19X-RAY DIFFRACTION1allR1
20X-RAY DIFFRACTION1allT1
21X-RAY DIFFRACTION1allU1
22X-RAY DIFFRACTION1allV1

+
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