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- PDB-7tqn: Structure of human TREX1 -

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Basic information

Entry
Database: PDB / ID: 7tqn
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 / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / MutSalpha complex binding / T cell antigen processing and presentation ...Regulation by TREX1 / immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / MutSalpha complex binding / T cell antigen processing and presentation / retrotransposition / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of lipid biosynthetic process / DNA modification / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / MutLalpha complex binding / cellular response to hydroxyurea / lymphoid progenitor cell differentiation / regulation of type I interferon production / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / 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 / regulation of immunoglobulin production / DNA catabolic process / apoptotic cell clearance / regulation of T cell activation / regulation of glycolytic process / DNA binding, bending / DNA metabolic process / DNA duplex unwinding / negative regulation of type I interferon-mediated signaling pathway / WW domain binding / type I interferon-mediated signaling pathway / 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 / protein-DNA complex / determination of adult lifespan / 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 / defense response to virus / DNA recombination / 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: 1.8 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)26,1801
Polymers26,1801
Non-polymers00
Water2,288127
1
A: Three-prime repair exonuclease 1

A: Three-prime repair exonuclease 1


Theoretical massNumber of molelcules
Total (without water)52,3602
Polymers52,3602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3300 Å2
ΔGint-3 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.081, 57.081, 123.117
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: 26180.080 Da / Num. of mol.: 1 / Mutation: A5T/P8H/P10H
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.: 127 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium chloride, 0.1 M Bis-Tris pH 5.5, 20% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→41.86 Å / Num. obs: 19529 / % possible obs: 99.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.044 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1133 / CC1/2: 0.488 / Rpim(I) all: 0.798

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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: 1.8→41.86 Å / SU ML: 0.1977 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 1948 10 %
Rwork0.175 17529 -
obs0.1783 19477 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 0 127 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791680
X-RAY DIFFRACTIONf_angle_d0.94552291
X-RAY DIFFRACTIONf_chiral_restr0.0586265
X-RAY DIFFRACTIONf_plane_restr0.0077294
X-RAY DIFFRACTIONf_dihedral_angle_d12.9253608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.30741350.27571210X-RAY DIFFRACTION97.53
1.85-1.90.28911330.21741199X-RAY DIFFRACTION98.67
1.9-1.950.26651360.19391225X-RAY DIFFRACTION99.05
1.95-2.010.24631360.19711222X-RAY DIFFRACTION99.2
2.01-2.090.24341350.18071227X-RAY DIFFRACTION99.13
2.09-2.170.22061360.17651219X-RAY DIFFRACTION98.83
2.17-2.270.2391380.17831244X-RAY DIFFRACTION99.14
2.27-2.390.19641380.15491238X-RAY DIFFRACTION99.49
2.39-2.540.20811390.16951247X-RAY DIFFRACTION99.64
2.54-2.730.21821400.17421257X-RAY DIFFRACTION99.64
2.73-3.010.21761410.18041273X-RAY DIFFRACTION99.93
3.01-3.440.19091390.17651259X-RAY DIFFRACTION99.22
3.44-4.340.15641460.15661314X-RAY DIFFRACTION100
4.34-41.860.21881560.17521395X-RAY DIFFRACTION99.61
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)
12.271421455960.244165928452-0.06713359411941.685637290560.6190502668622.352880489180.146494476370.0150960747352-0.2706282602890.258738609088-0.04064477124840.04214008133760.382271621204-0.111977419071-0.05323122631550.260026766988-0.01479379788510.01140090833850.2082139334980.004526073074640.212138441873-10.0182117513-4.70840213924-21.6305692513
22.88014436742-1.381768890340.5781679981712.04304024433-0.5364290471762.348298594920.1996194239070.0793437630107-0.7118864267050.192343944173-0.315070670280.08429944173680.6366870525950.2637536294660.03068272122720.4519444355040.04412882572720.02423869641620.278656696829-0.07746365555870.39533173786-2.90049047537-15.5103432055-34.1300221764
31.735951176340.9522461004660.2918853752121.419510838851.002946526671.921017747020.0784193988311-0.131549121568-0.007371038879820.112937643136-0.0417105843437-0.03608926604170.03464579292730.06327185525640.002088941287520.2094702604440.0142428109405-0.006326080424090.228797252122-0.008432598733770.192200993877-1.563548046286.9391541107-20.1722386395
42.62261414270.382140310628-0.2191418371262.578790121270.6747801675142.84259855475-0.0409789716645-0.197738564163-0.09284670926270.298344286763-0.08680878647130.1726496860880.0912308768178-0.2742755896620.1501240092320.237730030307-0.02081366250310.06273730795450.212641904377-0.03151640012130.260702170766-13.033325225-5.90385060552-21.2323349251
50.8559776545230.117455045435-0.5531157329174.039583915310.05614537688661.112409675430.05414789843310.0829626745450.100178927424-0.0422571768145-0.04298397423960.43334795536-0.121567592772-0.218527244277-0.03824310450530.2355130951810.01322739726130.01387434544050.260340504045-0.0369857518710.256577549916-14.86307936744.84944160086-16.8979092382
62.73259497992-1.178329782990.359335815811.72113587309-0.2627247927451.107259234370.0396251325363-0.305319740237-0.6849247984040.1374107815410.04635073922130.3352114557930.271947029368-0.0306567323608-0.08306740256640.314916314238-0.02328005542740.005663161587150.2617893478270.01119642011710.326570227252-6.78070260906-18.6214998269-17.4036934373
70.457700943936-1.38466495583-0.1148662341084.85759196849-0.5987663338681.2327005962-0.0202716545756-0.11187966179-0.07922558274260.29663776832-0.146514734533-0.6702911412980.1380773475080.2998087410060.08392116672190.2958078033810.0533720402264-0.006944064800790.2866219615190.02519941474550.3200262364212.1464834953-10.9105415841-22.8572552226
82.515154755930.5863961673280.2684692367611.37906029208-0.07723335633851.932335494190.14895949855-0.126929128318-0.09694101813810.322840070198-0.1288927490.1320994302930.23610657799-0.383460800315-0.01645491229310.227750074318-0.02664612296860.01529022587440.2421171379140.002684350829720.297891947164-16.0113011119-10.1093781441-19.3035848544
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 5 through 44 )5 - 441 - 40
22chain 'A' and (resid 45 through 64 )45 - 6441 - 52
33chain 'A' and (resid 65 through 114 )65 - 11453 - 102
44chain 'A' and (resid 115 through 129 )115 - 129103 - 117
55chain 'A' and (resid 130 through 150 )130 - 150118 - 138
66chain 'A' and (resid 151 through 187 )151 - 187139 - 166
77chain 'A' and (resid 188 through 208 )188 - 208167 - 187
88chain 'A' and (resid 209 through 236 )209 - 236188 - 215

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