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- PDB-7tqo: Structure of human TREX1 -

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Basic information

Entry
Database: PDB / ID: 7tqo
TitleStructure of human TREX1
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / nuclease / DNase / innate immunity / autoimmunity
Function / homology
Function and homology information


Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding ...Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / atrial cardiac muscle tissue development / activation of immune response / DNA synthesis involved in UV-damage excision repair / T cell antigen processing and presentation / MutSalpha complex binding / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of fatty acid metabolic process / regulation of lipid biosynthetic process / DNA modification / WW domain binding / heart process / MutLalpha complex binding / regulation of protein complex stability / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / macrophage activation involved in immune response / regulation of tumor necrosis factor production / IRF3-mediated induction of type I IFN / regulation of cellular respiration / inflammatory response to antigenic stimulus / DNA catabolic process / regulation of immunoglobulin production / apoptotic cell clearance / regulation of T cell activation / regulation of glycolytic process / DNA duplex unwinding / DNA binding, bending / 3'-5'-DNA exonuclease activity / negative regulation of type I interferon-mediated signaling pathway / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / type I interferon-mediated signaling pathway / blood vessel development / nuclear replication fork / cellular response to interferon-beta / mismatch repair / heart morphogenesis / mitotic G1 DNA damage checkpoint signaling / negative regulation of innate immune response / 3'-5' exonuclease activity / generation of precursor metabolites and energy / kidney development / determination of adult lifespan / protein-DNA complex / establishment of protein localization / cellular response to gamma radiation / cellular response to reactive oxygen species / nuclear envelope / single-stranded DNA binding / regulation of inflammatory response / double-stranded DNA binding / DNA recombination / defense response to virus / DNA replication / protein stabilization / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / 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
Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZhou, W. / Richmond-Buccola, D. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of human TREX1 DNA degradation and autoimmune disease.
Authors: Zhou, W. / Richmond-Buccola, D. / Wang, Q. / Kranzusch, P.J.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Three-prime repair exonuclease 1


Theoretical massNumber of molelcules
Total (without water)26,0971
Polymers26,0971
Non-polymers00
Water4,252236
1
A: Three-prime repair exonuclease 1

A: Three-prime repair exonuclease 1


Theoretical massNumber of molelcules
Total (without water)52,1942
Polymers52,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3240 Å2
ΔGint-3 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.592, 57.592, 124.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 26096.928 Da / Num. of mol.: 1 / Mutation: A5T, P8H, P10H, F17L, M19L, F26S, Q28R, K30E
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES-KOH pH 7.6, 10% PEG-8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.25→42.26 Å / Num. obs: 58943 / % possible obs: 99.8 % / Redundancy: 45.6 % / Biso Wilson estimate: 17.11 Å2 / CC1/2: 1 / Rpim(I) all: 0.017 / Net I/σ(I): 19
Reflection shellResolution: 1.25→1.27 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2773 / CC1/2: 0.449

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXJ

3mxj


Resolution: 1.25→42.26 Å / SU ML: 0.1335 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1895 2000 3.4 %
Rwork0.1712 56783 -
obs0.1719 58783 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.56 Å2
Refinement stepCycle: LAST / Resolution: 1.25→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1705 0 0 236 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071767
X-RAY DIFFRACTIONf_angle_d0.94232420
X-RAY DIFFRACTIONf_chiral_restr0.071283
X-RAY DIFFRACTIONf_plane_restr0.0109312
X-RAY DIFFRACTIONf_dihedral_angle_d13.3896653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.29871370.28453875X-RAY DIFFRACTION97.07
1.28-1.310.27341410.27223999X-RAY DIFFRACTION99.95
1.31-1.350.26441390.24973960X-RAY DIFFRACTION99.98
1.35-1.40.22811410.23624006X-RAY DIFFRACTION99.95
1.4-1.450.25651420.22644027X-RAY DIFFRACTION100
1.45-1.50.21841410.194020X-RAY DIFFRACTION99.95
1.5-1.570.20521410.17454009X-RAY DIFFRACTION100
1.57-1.660.20321430.17664041X-RAY DIFFRACTION100
1.66-1.760.18411420.17814041X-RAY DIFFRACTION100
1.76-1.90.1831430.17264050X-RAY DIFFRACTION100
1.9-2.090.17771430.15954089X-RAY DIFFRACTION99.98
2.09-2.390.15591460.15044115X-RAY DIFFRACTION99.91
2.39-3.010.18071470.16354160X-RAY DIFFRACTION100
3.01-42.260.18931540.16334391X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.046973921910.5786525195830.2572522807581.787181317650.8748374906982.163042340980.02923426474090.0307538228358-0.1030810253490.1793311847940.04594000586780.04856672322520.118047536401-0.0162611065048-0.07200780372260.172628136815-0.005040103611710.01274515847270.1135141524250.02553382328730.1423260307-10.5499316852-4.99921049364-22.2608059336
21.277224415830.1469542904960.3867843030251.252008292950.2860225226151.728035078580.0415522086931-0.0291942219984-0.1229568291390.2431404268710.00109015910473-0.07071477063320.2163209558750.137088603905-0.00842937721850.199297826476-0.000332570959458-0.0006115675480530.1651515226010.01447543602350.162190535310.939455319554-1.00888358561-22.2419243184
31.458453266451.324804317221.125694307523.541844962582.692824688984.5833723004-0.136522963963-0.008339988834250.197332787948-0.0524591254176-0.04099983624230.384543812394-0.29421230002-0.1786668474380.1370917088850.159794605930.0137384741133-0.004860536779440.13556359976-0.006472115653760.160734785389-11.69396053187.19284843857-28.6895434659
42.27929039429-0.06059072199050.3818932159251.86081502918-0.249006610022.955616475190.0378351779632-0.0737392521772-0.1129964175390.2391088474830.05176656514910.1294988165050.058152106797-0.156984152084-0.09886304437060.156885040478-0.01754743823770.02593441167020.115908765594-0.002556340448360.152216822244-13.089199125-5.88933724866-21.5037190581
51.039186539580.52755562921-0.2509851250793.11767445950.4457147135221.677783033820.114071055401-0.01832073082360.231712007004-0.110455853456-0.1093985403010.248863917126-0.20480507311-0.250226823929-0.002774849094180.2146777032190.0393918548760.03893647557790.1547897170290.001300939759470.184912052393-15.00391408284.930916461-16.7482615145
62.67759191687-0.6024674198680.966664667684.25530118281-0.7604316343632.882367775180.00861988048391-0.115289369919-0.4878259685510.1649547581520.1642857543610.1334760549630.401622938765-0.0581943775641-0.02723526566490.221915649776-0.03021601144990.01095130875110.1476314399080.01007910066430.231601430102-12.5129189081-17.8220635533-18.0674215059
70.9695407343550.0532184513169-0.3924125477971.70506458687-1.895265890475.095994767110.170170243141-0.343066916826-0.4621392688480.0857109684325-0.01291235993510.2594269414680.3838895906680.2217798492350.06353334244790.2364002398860.0277560946437-0.03412907664450.1914790821620.04860858455540.266543497778-1.66221666689-21.5039009982-15.9142127308
83.15952849226-2.247509978770.6008540664891.62751554254-0.7405631804182.39398691616-0.00647714752054-0.131387966878-0.1065224499820.0552560409480.00977971389718-0.6010844925850.03780007536540.398167656767-0.006998347322560.1733398148080.00486372520502-0.02056510441710.2085331790130.0001158102878930.2491771310612.51435557465-11.0380844584-23.1151637563
95.0697464054-0.441433910067-0.7541667407611.066435893710.07949659476611.266813767150.0192756223353-0.0530852204309-0.7918473746960.1442642459030.02708523633230.08230368193450.287962763448-0.117632903044-0.03964237645540.233989615036-0.0310539360763-0.02312115797490.156394291275-0.01818968030220.274272894565-14.177991386-19.1382779109-25.5552450894
102.935081587022.150343106821.829921127093.417414710952.392472568323.94304969032-0.0910435889868-0.2264955705340.334534809860.110838848677-0.1376555523940.381402953436-0.15375245641-0.3431269339060.1043253235710.2037294818980.01756146736620.04025844568220.181408711095-0.0119872219890.205429069375-18.50784763860.56031015412-12.6366071489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 44 )4 - 441 - 41
22chain 'A' and (resid 45 through 101 )45 - 10142 - 94
33chain 'A' and (resid 102 through 114 )102 - 11495 - 107
44chain 'A' and (resid 115 through 129 )115 - 129108 - 122
55chain 'A' and (resid 130 through 150 )130 - 150123 - 143
66chain 'A' and (resid 151 through 166 )151 - 166144 - 159
77chain 'A' and (resid 167 through 187 )167 - 187160 - 175
88chain 'A' and (resid 188 through 208 )188 - 208176 - 196
99chain 'A' and (resid 209 through 222 )209 - 222197 - 210
1010chain 'A' and (resid 223 through 237 )223 - 237211 - 225

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