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- PDB-6w10: Structure of mouse TREX1 with E198K disease-associated mutation -

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Basic information

Entry
Database: PDB / ID: 6w10
TitleStructure of mouse TREX1 with E198K disease-associated mutation
ComponentsThree-prime repair exonuclease 1
KeywordsHYDROLASE / nuclease / DNase / innate immunity / autoimmunity
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
Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80003386368 Å
AuthorsZhou, W. / Mohr, L. / Maciejowski, J. / Kranzusch, P.J.
CitationJournal: Mol.Cell / Year: 2021
Title: cGAS phase separation inhibits TREX1-mediated DNA degradation and enhances cytosolic DNA sensing.
Authors: Zhou, W. / Mohr, L. / Maciejowski, J. / Kranzusch, P.J.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Three-prime repair exonuclease 1


Theoretical massNumber of molelcules
Total (without water)52,8222
Polymers52,8222
Non-polymers00
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-2 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.579, 85.338, 99.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 26411.107 Da / Num. of mol.: 2 / Mutation: E198K
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NH4OAc, 17.5% PEG 3350

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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 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→46.082 Å / Num. obs: 52490 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.996 / Rpim(I) all: 0.044 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3071 / CC1/2: 0.694 / Rpim(I) all: 0.493 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXJ

3mxj


Resolution: 1.80003386368→46.0815723547 Å / SU ML: 0.207863400799 / Cross valid method: FREE R-VALUE / σ(F): 1.33660788442 / Phase error: 21.1759656496
RfactorNum. reflection% reflectionSelection details
Rfree0.203539892849 1998 3.81836945304 %Random selection
Rwork0.177648065152 ---
obs0.178623584216 52326 99.75217325 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.2082269278 Å2
Refinement stepCycle: LAST / Resolution: 1.80003386368→46.0815723547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 483 3835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009825380836553432
X-RAY DIFFRACTIONf_angle_d1.070304522124673
X-RAY DIFFRACTIONf_chiral_restr0.064429518203536
X-RAY DIFFRACTIONf_plane_restr0.00668381438978603
X-RAY DIFFRACTIONf_dihedral_angle_d13.49646530112106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8450.336415661651380.2930954864273471X-RAY DIFFRACTION97.5141853553
1.845-1.89490.3001169063221390.2378794914793550X-RAY DIFFRACTION99.8646453709
1.8949-1.95070.2351155779031420.2156510104443561X-RAY DIFFRACTION99.8382313292
1.9507-2.01370.2215097793641410.2052198060953537X-RAY DIFFRACTION99.9185004075
2.0137-2.08560.2358535377241420.192724886693576X-RAY DIFFRACTION99.9731110514
2.0856-2.16910.2054280570071410.1690734778183566X-RAY DIFFRACTION99.9730312837
2.1691-2.26790.2236504690581410.1803040986633564X-RAY DIFFRACTION100
2.2679-2.38740.2197168750261430.1730189267193584X-RAY DIFFRACTION99.8660235798
2.3874-2.5370.1894753286591430.1718754238483589X-RAY DIFFRACTION99.946438136
2.537-2.73280.1999339690171420.1778637676813589X-RAY DIFFRACTION99.973204716
2.7328-3.00780.1829056413191440.1775853345293614X-RAY DIFFRACTION99.9468085106
3.0078-3.44290.2139655135761440.176161292563633X-RAY DIFFRACTION99.8677948176
3.4429-4.33720.1813388647711460.1531594979073669X-RAY DIFFRACTION100
4.3372-46.0810.188907354781520.1774063530563825X-RAY DIFFRACTION99.8744349573
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)
11.439701815410.194479044091-0.1170468534571.73296432068-0.6830613853532.03024965442-0.0724387611-0.07228077822770.165518757596-0.06359445237790.1546371094860.280005494198-0.15402297532-0.268166158266-0.06473652729020.2013624121330.00466877971236-0.02215870395070.2006659864-0.001817348560180.213535442195-2.849038330952.555441532478.01108979153
23.85042389377-0.865198348228-0.5082538591081.447244846150.3041837665353.995136166110.00846706442896-0.05260047094590.435265750896-0.0481816125167-0.00859249425872-0.256049640798-0.08977137562720.7072603720150.02285075408710.2143480069240.005996937984850.02102537229970.2867864048250.01360732528610.24935371822312.2345474598-5.7697474061515.7481363383
31.58599285106-0.5946530488620.2200872924672.30765224479-0.48377549491.95261653905-0.050698524490.01865354330880.137466368749-0.1257111431420.0747295590764-0.0440988282414-0.101191158639-0.0614026678431-0.02845998168680.198766525382-0.0178016207837-0.001078562084260.1940760710480.001945465479020.1756104458020.731927168532.29801519821.99938067899
43.088470749360.298451503339-0.1838243521861.238183419140.1098908580341.066361956810.2148687696480.171403822306-0.2503944375480.245328557425-0.0854099589917-0.06814510201920.09496799326270.0102474969572-0.1071362615970.237904125681-0.0106014382384-0.01745841190610.158725085276-0.006237376946250.2174985749350.0254020500598-4.9424026414338.5518417776
51.906942782540.222434177241-0.4299733749872.156650657941.149959347053.39252511378-0.03571324659990.1841591533860.123344448696-0.0125513341912-0.006449287957960.0840155934945-0.0691136823145-0.2431137863090.06150141725070.2077503427140.00321752886293-0.000813103754430.2193967142410.02472265531950.194922978882-2.74409159301-3.2361842640626.3385123235
61.792783318881.076259030190.1151457043033.62354959106-0.2475797626151.31969344659-0.0211154666105-0.03563086721080.02195375753860.1471438190870.04206424828530.00783736788773-0.0543238038696-0.0953060615518-0.01366025608890.2001336320620.01061641169220.01443935995190.210127824643-0.007363290101480.173579628232-1.039021686291.1299699145536.9415045233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 234 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 30 )
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 234 )

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