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- PDB-3u3y: Mouse TREX1 D200H mutant -

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Open data


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Basic information

Entry
Database: PDB / ID: 3u3y
TitleMouse TREX1 D200H mutant
Components
  • 5'-D(*GP*AP*CP*G)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / Rnase H fold / 3' exonuclease / homodimer / HYDROLASE-DNA complex
Function / homology
Function and homology information


immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / MutSalpha complex binding ...immune response in brain or nervous system / adenyl deoxyribonucleotide binding / CD86 biosynthetic process / immune complex formation / cellular response to type I interferon / organ or tissue specific immune response / 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 / regulation of immunoglobulin production / 3'-5'-DNA exonuclease activity / macrophage activation involved in immune response / regulation of tumor necrosis factor production / regulation of T cell activation / DNA catabolic process / regulation of cellular respiration / negative regulation of cGAS/STING signaling pathway / inflammatory response to antigenic stimulus / apoptotic cell clearance / 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 / regulation of innate immune response / blood vessel development / nuclear replication fork / cellular response to interferon-beta / heart morphogenesis / mitotic G1 DNA damage checkpoint signaling / response to UV / negative regulation of innate immune response / 3'-5' exonuclease activity / kidney development / DNA damage checkpoint signaling / protein-DNA complex / determination of adult lifespan / generation of precursor metabolites and energy / establishment of protein localization / cellular response to gamma radiation / cellular response to reactive oxygen species / cellular response to UV / single-stranded DNA binding / cellular response to oxidative stress / regulation of inflammatory response / double-stranded DNA binding / regulation of gene expression / defense response to virus / adaptive immune response / DNA replication / protein stabilization / inflammatory response / immune 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-BUTANEDIOL / DNA / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
CitationJournal: Dna Repair / Year: 2012
Title: Defects in DNA degradation revealed in crystal structures of TREX1 exonuclease mutations linked to autoimmune disease.
Authors: Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Three prime repair exonuclease 1
A: Three prime repair exonuclease 1
C: 5'-D(*GP*AP*CP*G)-3'
D: 5'-D(*GP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0697
Polymers69,8994
Non-polymers1703
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-32 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.066, 57.861, 68.227
Angle α, β, γ (deg.)90.00, 108.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33733.453 Da / Num. of mol.: 2 / Mutation: D200H
Source method: isolated from a genetically manipulated source
Details: expressed as N-term MBP fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: DNA chain 5'-D(*GP*AP*CP*G)-3'


Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized DNA oligonucleotide
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 16% PEG 4000, 0.1 M MES pH 6.0, 2% 1,4-butanediol, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 6, 2008 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→40 Å / Num. obs: 21089 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→22.724 Å / SU ML: 0.74 / σ(F): 1.33 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1136 5.16 %random
Rwork0.2131 ---
obs0.2162 22013 99.21 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.133 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.9029 Å20 Å2-2.5951 Å2
2--4.2174 Å2-0 Å2
3---3.6855 Å2
Refinement stepCycle: LAST / Resolution: 2.28→22.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 162 8 183 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073655
X-RAY DIFFRACTIONf_angle_d1.0965011
X-RAY DIFFRACTIONf_dihedral_angle_d17.2691372
X-RAY DIFFRACTIONf_chiral_restr0.057567
X-RAY DIFFRACTIONf_plane_restr0.006624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.38370.32761590.27022544X-RAY DIFFRACTION99
2.3837-2.50920.35361570.23932618X-RAY DIFFRACTION99
2.5092-2.66620.29731310.22872559X-RAY DIFFRACTION100
2.6662-2.87170.29141480.21092626X-RAY DIFFRACTION100
2.8717-3.160.28811260.20532622X-RAY DIFFRACTION100
3.16-3.61560.30421340.21982657X-RAY DIFFRACTION100
3.6156-4.54930.25361350.20692628X-RAY DIFFRACTION99
4.5493-22.72470.22491460.19652623X-RAY DIFFRACTION97
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)
12.11090.98810.18744.27690.64961.93520.267-0.0161-0.7955-0.3465-0.2817-0.13880.0651-0.16760.01650.1977-0.007-0.06340.22630.02490.356-6.6582-19.856112.2934
23.0415-0.4610.11473.9776-0.72921.68680.0388-0.2918-0.4587-0.227-0.02630.32440.1321-0.1538-0.03570.1885-0.038-0.03830.208-0.02290.1132-7.5011-7.618212.127
36.9754-1.0297-6.49570.2430.4968.3443-0.3804-0.5709-0.57480.1679-0.38020.73780.7507-0.31020.74720.3797-0.13510.07530.54210.14051.2128-0.2224-29.194524.108
44.9463-1.54952.96015.9313-1.84942.83580.43920.2019-0.31920.2928-0.4921-0.38340.36370.1978-0.08510.456-0.0256-0.11060.65430.23920.4456-1.164-21.424834.0004
50.44190.1066-1.18350.2803-0.37363.20020.2405-0.9075-0.35460.3715-0.0627-0.0739-0.0431-0.3032-0.07590.2322-0.106-0.04640.41950.07940.20046.9576-18.753118.3358
63.1863-1.737-0.24353.79140.42641.6094-0.1964-0.31590.20390.31820.00110.0267-0.0225-0.210.20160.27320.0016-0.03460.1819-0.0180.1696-5.75392.808912.803
72.9306-2.81712.10457.2051-1.0263.9421-0.4579-0.23160.43170.47280.41650.33650.3597-0.6536-0.08060.2061-0.0066-0.01020.3118-0.04020.2276-4.48775.703815.6246
86.5628-0.2956-3.39786.06414.13764.57420.21570.60980.89370.38520.0283-0.1202-0.1953-0.4331-0.08530.3891-0.0319-0.0310.26660.08180.28481.90616.05527.6238
90.2363-0.20150.11860.1978-0.17760.26720.11780.2413-0.1589-0.10360.0233-0.0230.08290.0580.19260.30010.155-0.15090.4841-0.13960.13980.7004-9.76661.3743
103.1458-0.09620.52273.19560.99751.5772-0.0328-0.0643-0.5481-0.1690.09430.32890.01290.1229-0.0160.2612-0.0387-0.08330.16550.00120.3266-8.1542-15.806210.3664
113.6449-3.14431.43594.19871.6237.20250.39850.40540.4251-1.1012-0.26250.4406-0.03850.25460.160.39360.0613-0.12790.3826-0.13150.399-9.9075-5.9315-0.2104
125.45971.2447-3.80933.96860.3795.2451-0.3935-0.2751-0.2565-0.57170.01120.1544-0.16720.37840.37050.231-0.0589-0.08190.37160.0430.5288-7.9445-17.18962.2253
130.19270.6993-0.76815.4022-0.72924.544-0.1-0.0394-0.380.1641-0.17230.44870.1107-0.1250.24270.2566-0.07870.03320.49730.19370.5098-15.7392-19.783121.5721
142.25592.0276-1.42642.1709-0.51312.5937-0.13730.0147-0.72330.1107-0.1789-0.29230.476-0.20410.28130.4955-0.18110.22280.69690.17151.1553-17.269-23.472429.0479
150.314-0.25220.0251.77950.81830.44840.0878-0.1296-0.06340.4188-0.12230.59850.12-0.2418-0.17160.2713-0.09070.06380.6070.23450.4626-11.6608-14.922331.306
163.80841.64530.18961.88742.25654.0278-0.6994-0.42260.0559-0.0071-0.2081-0.2314-0.16330.3750.730.4716-0.0961-0.0890.72740.21880.3691-3.2234-7.96129.9944
176.91972.2530.16673.2355-2.40872.8824-0.0761-0.4495-0.060.40630.18740.1683-0.4603-0.0214-0.14610.2503-0.01080.02280.34360.00820.0965-2.7314-8.570121.7094
182.04691.6417-2.42541.4016-1.78043.1915-0.0075-0.3889-0.45590.4116-0.02030.38350.07510.21490.09890.3287-0.01750.08730.53710.19190.4219-5.3046-20.535425.9116
194.84120.17872.03840.50671.56225.27440.12710.0894-1.57750.15610.013-0.06530.7158-0.1751-0.51050.281-0.0571-0.11480.34040.06330.9105-10.5874-28.210218.9041
200.006-0.0588-0.09680.57230.88891.3943-0.17490.0823-0.2852-0.4399-0.01610.6524-0.2206-0.29280.29960.3162-0.0668-0.19470.3003-0.02380.5616-16.2368-13.6774.7846
212.7827-0.5025-0.96760.09140.17510.3356-0.09430.1001-0.0396-0.31880.038-0.2937-0.30820.4766-0.12850.5942-0.23680.28920.58710.3040.72422.39188.91634.0834
227.4954-5.4750.68767.4817-0.41133.11690.3674-0.10150.4792-0.3411-0.30650.1523-0.0762-0.0519-0.11090.1726-0.05040.01780.3301-0.02420.190719.7196-9.648813.307
233.43621.0401-0.32040.98440.80471.58390.19730.4105-0.1913-0.4241-0.3714-0.22260.32370.24450.10780.23750.08140.02670.24410.03590.102918.7294-13.341411.5296
242.17030.93690.43681.58390.05280.8537-0.153-0.06830.5439-0.0639-0.01340.0354-0.27520.07440.36030.4717-0.1478-0.38430.44170.06130.981312.40319.523514.1595
253.55091.26642.26260.4570.67494.0332-0.278-0.27960.4639-0.12460.05790.1964-0.321-0.66890.66170.43410.1092-0.22770.6481-0.25130.523514.00647.176431.6897
264.83042.0921.03453.3687-3.06255.22450.1209-0.79830.29180.47210.04650.0732-0.79350.1654-0.27470.30260.1003-0.01970.5514-0.05350.26235.52081.96419.9324
273.9945-2.08371.41212.935-1.84772.66290.1809-0.0908-0.6228-0.0064-0.187-0.06780.53330.2292-0.13240.286-0.0272-0.07510.22890.04360.225416.9503-21.657115.7439
283.3039-0.47961.37617.3523-1.43030.78110.46060.079-1.3375-0.459-0.04260.37840.3110.0066-0.18380.3970.0659-0.14430.256-0.02060.558911.2536-26.355910.515
291.97650.0428-0.14751.77770.76961.82640.21230.47440.1185-0.74860.16330.0787-0.04780.2033-0.05250.40520.11480.03410.40720.04920.153710.204-8.18951.738
305.51180.35381.57414.5678-1.70434.95010.34640.41730.28370.13510.0889-0.1263-0.41370.1164-0.18670.1761-0.03480.12780.35290.0370.324722.7001-3.06711.0907
311.7235-0.9645-3.70936.8659-0.29168.89360.24160.33930.1615-0.098-0.4746-0.1788-0.07220.95660.08260.33370.10280.05380.45380.07820.190725.2336-13.00777.0213
320.18290.0083-0.25241.9307-0.96680.81920.01890.2116-0.1375-0.6738-0.2415-0.24480.44560.12550.14160.57770.27020.10140.8282-0.07860.328418.9177-16.5261-3.6273
335.53071.10711.17172.8581-1.32812.25240.03180.6540.6541-0.4677-0.1159-0.45190.16780.4959-0.29310.18960.07340.08890.54620.1330.454523.2567-2.59796.9194
346.51761.23962.44460.25180.65453.1427-0.1318-0.08190.71870.0720.1372-0.1956-0.16040.21360.15550.3495-0.0296-0.2640.4880.05261.387930.48684.693924.1183
350.18740.00980.25460.00590.01680.3445-0.0206-0.0670.09780.06820.0272-0.0633-0.0320.09210.23750.16530.1019-0.37780.6136-0.23440.406324.5159-2.716928.1841
360.3221-0.74970.19823.59950.94421.19220.1584-0.35710.47290.2013-0.17940.0847-0.3815-0.0740.23150.61220.0147-0.0170.4125-0.21260.362118.9235-3.81434.2798
374.7553-2.191-0.36522.3367-0.55994.1666-0.012-0.54610.38340.40570.2311-0.24280.2845-0.0698-0.14810.2189-0.0571-0.06170.374-0.02540.154415.9297-7.961522.4308
381.32481.4685-0.60551.6477-0.57540.6907-0.2242-0.1040.68810.1354-0.0588-0.2011-0.31880.11240.32140.30040.0254-0.25360.2797-0.16590.854319.8068.033922.3534
390.12860.1397-0.20680.1517-0.22630.33570.0655-0.05840.42020.078-0.13820.1531-0.21030.1043-0.47540.3798-0.15560.12260.31030.17171.066425.15536.528411.0519
402.0124-0.0582-0.79450.6982-0.82971.35220.28290.68280.5602-0.2899-0.0884-0.1473-0.3242-0.37170.05520.36750.22870.17740.6880.21980.316428.6297-10.53872.8528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:21)
2X-RAY DIFFRACTION2(chain A and resid 22:41)
3X-RAY DIFFRACTION3(chain A and resid 42:52)
4X-RAY DIFFRACTION4(chain A and resid 53:59)
5X-RAY DIFFRACTION5(chain A and resid 60:66)
6X-RAY DIFFRACTION6(chain A and resid 67:83)
7X-RAY DIFFRACTION7(chain A and resid 84:90)
8X-RAY DIFFRACTION8(chain A and resid 91:99)
9X-RAY DIFFRACTION9(chain A and resid 100:112)
10X-RAY DIFFRACTION10(chain A and resid 113:134)
11X-RAY DIFFRACTION11(chain A and resid 135:142)
12X-RAY DIFFRACTION12(chain A and resid 143:153)
13X-RAY DIFFRACTION13(chain A and resid 154:161)
14X-RAY DIFFRACTION14(chain A and resid 162:174)
15X-RAY DIFFRACTION15(chain A and resid 175:188)
16X-RAY DIFFRACTION16(chain A and resid 189:194)
17X-RAY DIFFRACTION17(chain A and resid 195:204)
18X-RAY DIFFRACTION18(chain A and resid 205:210)
19X-RAY DIFFRACTION19(chain A and resid 211:222)
20X-RAY DIFFRACTION20(chain A and resid 223:234)
21X-RAY DIFFRACTION21(chain B and resid 6:11)
22X-RAY DIFFRACTION22(chain B and resid 12:25)
23X-RAY DIFFRACTION23(chain B and resid 26:40)
24X-RAY DIFFRACTION24(chain B and resid 41:45)
25X-RAY DIFFRACTION25(chain B and resid 46:58)
26X-RAY DIFFRACTION26(chain B and resid 59:64)
27X-RAY DIFFRACTION27(chain B and resid 65:90)
28X-RAY DIFFRACTION28(chain B and resid 91:100)
29X-RAY DIFFRACTION29(chain B and resid 101:117)
30X-RAY DIFFRACTION30(chain B and resid 118:127)
31X-RAY DIFFRACTION31(chain B and resid 128:139)
32X-RAY DIFFRACTION32(chain B and resid 140:145)
33X-RAY DIFFRACTION33(chain B and resid 146:157)
34X-RAY DIFFRACTION34(chain B and resid 158:175)
35X-RAY DIFFRACTION35(chain B and resid 176:187)
36X-RAY DIFFRACTION36(chain B and resid 188:191)
37X-RAY DIFFRACTION37(chain B and resid 192:208)
38X-RAY DIFFRACTION38(chain B and resid 209:214)
39X-RAY DIFFRACTION39(chain B and resid 215:224)
40X-RAY DIFFRACTION40(chain B and resid 225:234)

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