[English] 日本語
Yorodumi
- PDB-9o0x: Co-crystal structure of human TREX1 in complex with an inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o0x
TitleCo-crystal structure of human TREX1 in complex with an inhibitor
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE/INHIBITOR / TREX1 / SGC / TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Structural Genomics Consortium / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / : / immune complex formation / 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 ...Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / : / immune complex formation / 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 modification / regulation of lipid biosynthetic process / regulation of fatty acid metabolic process / regulation of protein complex stability / cellular response to hydroxyurea / heart process / 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 / IRF3-mediated induction of type I IFN / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / 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 / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / mismatch repair / cellular response to interferon-beta / heart morphogenesis / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / 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 / nuclear envelope / single-stranded DNA binding / double-stranded DNA binding / regulation of inflammatory response / DNA recombination / defense response to virus / DNA replication / protein stabilization / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / 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
: / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsDehghani-Tafti, S. / Dong, A. / Li, Y. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Co-crystal structure of human TREX1 in complex with an inhibitor
Authors: Dehghani-Tafti, S. / Dong, A. / Li, Y. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: 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
C: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,27235
Polymers75,5103
Non-polymers1,76232
Water5,909328
1
A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,59728
Polymers50,3402
Non-polymers1,25726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4490 Å2
ΔGint-7 kcal/mol
Surface area16180 Å2
MethodPISA
2
B: Three-prime repair exonuclease 1
C: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47321
Polymers50,3402
Non-polymers1,13319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-14 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.049, 153.457, 137.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-313-

UNX

21B-482-

HOH

-
Components

-
Protein , 1 types, 3 molecules ABC

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


Mass: 25169.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III

-
Non-polymers , 5 types, 360 molecules

#2: Chemical ChemComp-A1B7U / 5-({N-[(2,3-dichlorophenyl)methyl]-3,5-difluorobenzamido}methyl)-3-(methylamino)pyridine-2-carboxylic acid


Mass: 480.291 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H17Cl2F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG 600, 0.15M KSCN, 0.1M Tris 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 94939 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Rrim(I) all: 0.079 / Χ2: 0.977 / Net I/σ(I): 8.6 / Num. measured all: 788428
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.68-1.717.80.97546840.7950.9410.361.0410.66599.4
1.71-1.747.70.78746850.8440.9570.2940.8410.67699.7
1.74-1.777.40.67846600.8810.9680.260.7270.67599.1
1.77-1.817.10.53646800.8960.9720.2120.5780.69298.8
1.81-1.858.30.43846890.9530.9880.1580.4670.70599.7
1.85-1.898.50.38347100.9590.9890.1370.4070.72699.9
1.89-1.948.50.31847260.970.9920.1130.3380.74100
1.94-1.998.50.2647190.980.9950.0930.2770.76799.9
1.99-2.058.50.2247320.9860.9960.0790.2340.774100
2.05-2.128.50.17447190.990.9970.0630.1850.813100
2.12-2.198.50.13847410.9930.9980.050.1470.844100
2.19-2.288.40.11447370.9950.9990.0410.1210.863100
2.28-2.388.30.09647460.9960.9990.0350.1020.92100
2.38-2.517.50.08447310.9960.9990.0320.090.96399.7
2.51-2.678.50.07247610.9980.9990.0260.0771.02599.9
2.67-2.879.20.06547670.99810.0230.0691.159100
2.87-3.169.10.05448050.99910.0190.0571.334100
3.16-3.6290.04648030.99910.0160.0491.49599.8
3.62-4.568.30.0448430.99910.0150.0431.59499.8
4.56-508.40.0450010.99910.0140.0421.79199.7
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→49.15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.278 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1902 2 %RANDOM
Rwork0.19691 ---
obs0.19774 92999 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0 Å2
2--0.18 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.68→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 137 328 5157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125085
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164735
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.8146972
X-RAY DIFFRACTIONr_angle_other_deg0.4811.72810912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.007530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76510725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021095
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.3392.6092601
X-RAY DIFFRACTIONr_mcbond_other6.3342.6092601
X-RAY DIFFRACTIONr_mcangle_it9.4934.6673267
X-RAY DIFFRACTIONr_mcangle_other9.4944.6683268
X-RAY DIFFRACTIONr_scbond_it6.6492.7872484
X-RAY DIFFRACTIONr_scbond_other6.6482.7872485
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.8015.0543706
X-RAY DIFFRACTIONr_long_range_B_refined15.15726.145588
X-RAY DIFFRACTIONr_long_range_B_other14.51925.535503
X-RAY DIFFRACTIONr_rigid_bond_restr3.25239820
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.721 Å
RfactorNum. reflection% reflection
Rfree0.266 138 -
Rwork0.219 6571 -
obs--95.52 %

+
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