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- PDB-7tqp: Structure of human TREX1 -

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Basic information

Entry
Database: PDB / ID: 7tqp
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 / 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 ...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 / DNA modification / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / lymphoid progenitor cell differentiation / regulation of type I interferon production / regulation of lysosome organization / cellular response to hydroxyurea / 3'-5'-DNA exonuclease activity / regulation of cellular respiration / regulation of tumor necrosis factor production / MutLalpha complex binding / inflammatory response to antigenic stimulus / macrophage activation involved in immune response / regulation of immunoglobulin production / IRF3-mediated induction of type I IFN / DNA catabolic process / regulation of T cell activation / apoptotic cell clearance / regulation of glycolytic process / negative regulation of type I interferon-mediated signaling pathway / DNA binding, bending / WW domain binding / type I interferon-mediated signaling pathway / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / heart morphogenesis / mismatch repair / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / determination of adult lifespan / generation of precursor metabolites and energy / cellular response to reactive oxygen species / kidney development / establishment of protein localization / protein-DNA complex / cellular response to gamma radiation / 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: 1.95 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

Downloads & links

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Assembly

Deposited unit
A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6655
Polymers26,2811
Non-polymers3844
Water2,468137
1
A: Three-prime repair exonuclease 1
hetero molecules

A: Three-prime repair exonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,33110
Polymers52,5622
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4620 Å2
ΔGint-97 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.582, 57.582, 125.757
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: 26281.133 Da / Num. of mol.: 1
Mutation: A5T, P8H, P10H, F17L, M19L, F26S, Q28R, K30E, C42R, S46N, P47T, P48S, T49I, P53H, T56P, P59R
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 37.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M CHES pH 9.5, 1.26 M (NH4)2SO4

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→42.47 Å / Num. obs: 16216 / % possible obs: 99.9 % / Redundancy: 21.6 % / Biso Wilson estimate: 32.92 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.049 / Net I/σ(I): 9.7
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1098 / CC1/2: 0.403

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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: 1.95→42.47 Å / SU ML: 0.2517 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 1611 10 %
Rwork0.2045 14494 -
obs0.207 16105 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 20 137 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211717
X-RAY DIFFRACTIONf_angle_d0.58042343
X-RAY DIFFRACTIONf_chiral_restr0.0393267
X-RAY DIFFRACTIONf_plane_restr0.004300
X-RAY DIFFRACTIONf_dihedral_angle_d12.4769626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.36941270.31761146X-RAY DIFFRACTION97.47
2.01-2.070.28721310.25341180X-RAY DIFFRACTION99.77
2.07-2.150.27841340.23961194X-RAY DIFFRACTION99.92
2.15-2.230.25991300.23721172X-RAY DIFFRACTION99.92
2.23-2.330.2581320.22281192X-RAY DIFFRACTION99.85
2.33-2.460.22391320.20721185X-RAY DIFFRACTION100
2.46-2.610.26561330.22681204X-RAY DIFFRACTION100
2.61-2.810.22951330.21711195X-RAY DIFFRACTION99.92
2.81-3.090.28661340.20391203X-RAY DIFFRACTION100
3.1-3.540.22041370.19461238X-RAY DIFFRACTION99.93
3.54-4.460.17041380.17031242X-RAY DIFFRACTION100
4.46-42.470.21791500.19831343X-RAY DIFFRACTION99.93
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)
12.640475906450.4634793068580.2053867184172.495872640220.4912977795192.19876691608-0.0562655814234-0.0246410610902-0.1166994167970.07745767209510.09212871625560.04555800647670.0343147697955-0.0984358684651-0.01543356448960.2561441973690.02535798420010.01119850401080.2493883323090.01776128042940.27967385012-9.81318748395-4.42938427449-22.6121102465
24.60491106062-3.815570395881.902235900528.68224253401-3.017819357732.6137199932-0.02323799852940.127167326797-0.5964130522910.165540615951-0.1211884024820.2059910066751.151745079220.2534350292670.1374649950390.5966691473540.1545946853920.06324306998030.488470248372-0.07625396006420.389116357622-2.21628385539-16.4272387504-34.6128977371
31.628880325330.7492438835280.4449498672971.484173742560.4662608366141.41232301818-0.00735216662696-0.0398701788487-0.03959798431520.1108564833750.03254127090340.107481958591-0.01205360728960.00258999033285-0.03358023528810.2442985111940.01643754685520.02554903735880.2208988904790.001411192078550.228500061431-4.547361674423.74823091719-21.0840551965
41.79941565618-0.4281990928780.2551849163032.83280468699-0.3543961724921.314501673490.0691464861704-0.0181820688636-0.1598729581650.125732151419-0.07278790869260.3742952754240.0601374656776-0.0939047260931-0.01840389589630.297933343813-0.01503912264130.02273256844720.3054094940550.01110339991530.229732043583-9.8154871464-9.73836196331-17.3207547304
51.15543169334-2.465333207580.1403122834026.37731905129-1.412203260263.91913964376-0.0331503654364-0.19833828476-0.1176167766110.0548701017495-0.0721904566889-0.7597918299830.09064450360340.7594898051740.1381649330970.3709849932020.0431639683770.009513468447350.4395720529290.03529880577840.347960784871.98957734486-10.828572614-23.2342379238
62.590110177781.085222674160.1353459549852.405481181220.505964040552.233717106650.05899939815660.120932700026-0.03169520862560.308787779959-0.1594726791270.3724743349760.283790713504-0.3763652411340.07277560019960.269602390082-0.0306167457223-0.007593496666180.2622476957470.03592780071930.298610391532-15.9986585929-9.9970709805-19.8842928152
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 6 through 44 )6 - 441 - 39
22chain 'A' and (resid 45 through 64 )45 - 6440 - 52
33chain 'A' and (resid 65 through 129 )65 - 12953 - 117
44chain 'A' and (resid 130 through 187 )130 - 187118 - 168
55chain 'A' and (resid 188 through 208 )188 - 208169 - 189
66chain 'A' and (resid 209 through 236 )209 - 236190 - 217

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