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- PDB-3u6f: Mouse TREX1 D200N mutant -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3u6f
TitleMouse TREX1 D200N mutant
Components
  • 5'-D(*GP*AP*CP*G)-3'
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / RNase H fold / 3' exonuclease / HYDROLASE-DNA complex
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 / MutSalpha complex binding ...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 / DNA exonuclease activity / DNA modification / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of fatty acid metabolic process / heart process / regulation of protein complex stability / glycoprotein biosynthetic process / 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 / DNA catabolic process / regulation of T cell activation / apoptotic cell clearance / cGAS/STING signaling pathway / 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 / regulation of innate immune response / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / blood vessel development / nuclear replication fork / response to UV / heart morphogenesis / cellular response to interferon-beta / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / DNA damage checkpoint signaling / 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 / cellular response to UV / single-stranded DNA binding / regulation of gene expression / regulation of inflammatory response / cellular response to oxidative stress / double-stranded DNA binding / defense response to virus / adaptive immune response / DNA replication / protein stabilization / immune response / inflammatory response / innate immune response / DNA damage response / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / DNA binding / identical protein binding / nucleus / cytoplasm / cytosol
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: 2.3 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 12, 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.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)70,0798
Polymers69,8504
Non-polymers2294
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-24 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.886, 56.644, 68.143
Angle α, β, γ (deg.)90.00, 107.97, 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: 33709.406 Da / Num. of mol.: 2 / Mutation: D200N
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: DNA chain 5'-D(*GP*AP*CP*G)-3'


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


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.71 Å3/Da / Density % sol: 27.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M MES, 0.075M NaCl, 12% PEG 3350, 5% 1,4-butanediol, 2mM CaCl2, pH 5.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 25, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→33 Å / Num. all: 21121 / Num. obs: 21073 / % possible obs: 99.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.221 Å / SU ML: 0.72 / σ(F): 0 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1082 5.13 %random
Rwork0.2193 ---
obs0.2227 21073 99.77 %-
all-21121 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.148 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.1132 Å20 Å2-2.2616 Å2
2--5.6214 Å2-0 Å2
3---3.4918 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 162 14 176 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083625
X-RAY DIFFRACTIONf_angle_d1.2734966
X-RAY DIFFRACTIONf_dihedral_angle_d17.4981355
X-RAY DIFFRACTIONf_chiral_restr0.059564
X-RAY DIFFRACTIONf_plane_restr0.008616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40460.39011350.29792474X-RAY DIFFRACTION100
2.4046-2.53140.34871170.27652523X-RAY DIFFRACTION100
2.5314-2.68990.38241430.26862481X-RAY DIFFRACTION100
2.6899-2.89750.36811410.27242455X-RAY DIFFRACTION100
2.8975-3.18890.33261500.25132470X-RAY DIFFRACTION100
3.1889-3.64980.27761270.23142516X-RAY DIFFRACTION100
3.6498-4.59640.24771360.16752530X-RAY DIFFRACTION100
4.5964-33.22420.221330.18712542X-RAY DIFFRACTION99
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)
12.2293-0.9001-0.01741.8231-0.16120.61030.02230.7623-0.6130.0234-0.08020.15250.1616-0.07020.03950.3088-0.0444-0.03180.6506-0.250.3217-7.8729-16.629512.2956
22.2271-1.2412-1.30931.43991.12151.37270.28640.8702-0.0739-0.3008-0.41010.2167-0.1807-0.20070.03720.2608-0.0156-0.01620.6713-0.04450.1622-6.3526-7.642811.4149
33.98562.93721.05948.1399-4.48094.9139-0.5479-0.4414-0.93870.3730.0033-1.0480.6959-0.58640.54980.5026-0.0123-0.0710.5432-0.15970.71220.6544-29.547617.6644
44.86892.7347-2.09624.1358-3.00642.18860.72610.7288-0.21020.0004-0.3774-0.2957-0.2782-0.1188-0.3170.5471-0.0277-0.04480.45670.08830.374-2.9011-25.382634.8771
50.49251.64480.60657.49871.84990.7625-0.1842-1.1784-0.42040.99310.6129-0.32930.4481.5922-0.44540.40380.0736-0.0530.71060.15150.29063.148-20.42428.3803
60.9830.326-0.54670.38860.25770.9943-0.01020.46570.1462-0.0530.1063-0.0059-0.0363-0.1421-0.16120.25220.0148-0.08740.5234-0.00480.1598-0.8676-4.924912.5347
71.6154-0.5666-1.1493.6568-2.45893.8092-0.25591.24690.9562-0.0576-0.168-0.4054-0.52820.17380.38340.4187-0.0418-0.11910.590.19520.3786-2.33376.048213.8758
83.1493.901-0.82485.1988-1.74731.6490.34421.68910.4052-0.4131-0.09970.0265-0.1499-0.1891-0.18560.4660.2957-0.02781.26370.29590.3269-1.6762-1.24750.8036
92.0683-1.3713-0.183.0105-1.81424.04710.35391.1857-0.0999-0.6988-0.51220.08880.2066-0.23560.05560.32670.2228-0.0151.0136-0.17360.08682.1364-12.78411.7896
107.10480.5449-2.21490.0418-0.16950.6904-0.12451.888-0.9627-0.38320.05970.1033-0.0404-0.7563-0.02730.32690.0996-0.00480.843-0.45520.58642.1592-23.82915.8952
111.9374-0.21252.1712.39340.68093.06510.15950.647-0.1971-0.0334-0.49930.2128-0.0856-0.54520.2120.20920.0147-0.0460.6409-0.19930.3454-12.519-12.710811.164
120.6423-1.47220.65863.5705-2.40674.89940.4811.28120.2901-0.5575-0.36710.0566-0.408-1.0742-0.06820.3770.25010.06751.2630.10590.3484-9.4441-5.1357-0.466
132.94030.2267-2.23053.97762.37434.44750.33391.3736-0.2272-0.733-0.27570.1293-0.35830.0307-0.10410.36590.1302-0.01211.1217-0.35450.3808-7.1806-16.27260.3152
146.47542.9210.09616.8258-2.59564.22030.06290.1464-0.65180.5638-0.1459-0.17160.0439-0.1930.03770.3257-0.13470.13510.2936-0.12420.5475-15.2954-21.365522.6986
155.6407-0.5908-3.05910.40020.96542.8879-0.8382-0.0919-1.29540.56980.4930.45421.2285-0.43090.33540.6104-0.13260.39380.54760.05830.5945-18.2821-16.799729.2669
163.4655-3.32243.29523.8802-2.64943.5093-0.3048-0.7362-0.32360.82520.26290.4001-0.39290.11380.0580.4149-0.04550.07350.40560.04660.186-9.4512-15.13631.0457
177.30335.6082-5.44346.3207-5.72765.76260.2365-0.5099-0.17571.1659-0.1837-0.3111-0.60060.0572-0.04410.652-0.0479-0.0670.6769-0.04820.2226-4.1348-10.328432.1413
183.02121.4436-0.88894.774-5.21516.82860.08840.1421-0.00321.0809-0.1940.2948-0.5415-0.14680.10380.2818-0.00920.06720.3337-0.04960.1725-3.7523-13.947223.3382
191.51850.21641.2541.86192.32643.55530.16870.243-0.55110.372-0.44760.78350.5052-0.56910.18250.3596-0.12520.11130.5528-0.42640.8343-11.294-27.381916.8419
203.7816-1.79040.24563.68811.460.89240.50571.1291-0.8683-0.7748-0.85011.14940.0694-0.08740.4180.32380.1338-0.22530.8455-0.39780.4934-16.7787-11.23983.8125
212.72641.7045-0.43921.8876-0.05663.00950.37880.6751.404-0.88-0.2086-0.8206-0.59810.3069-0.11560.61660.01820.22840.75480.48390.831518.12873.70247.9368
224.7604-1.74671.98442.6361-1.55781.95530.57031.2539-0.1572-0.3631-0.6927-0.15410.10610.13140.05940.27740.0401-0.01360.5950.0480.132521.019-15.948712.8863
232.3739-0.66590.75511.75980.78634.175-0.4460.35891.71730.11850.2089-0.2516-0.3667-0.13410.25290.5878-0.0611-0.34620.65250.31331.240911.8198.975319.2807
244.74640.42671.71872.4771.94291.9324-0.2107-0.43190.7243-0.24950.25380.03-0.3843-0.56180.03610.3921-0.0549-0.20460.31870.08870.684612.07562.95130.0072
254.7915-0.08781.22650.0019-0.07632.4452-0.00351.22190.0815-0.04940.1306-0.33980.10330.3930.03950.1821-0.0421-0.00540.64860.06510.15211.3242-13.533412.417
262.9474-1.29452.44342.1446-0.75012.1509-0.3639-0.0674-0.3364-0.1116-0.06750.0294-1.25630.39860.44640.3513-0.0003-0.02780.3379-0.00450.233221.1357-24.06521.2164
275.5185-3.89792.30285.1062-0.50911.48990.55581.0949-1.618-0.30180.01360.37580.23860.6142-0.48830.39940.001-0.03670.6032-0.47380.974411.392-27.961412.3103
282.5721-1.91190.57281.60860.33773.19930.72471.27910.0751-0.5325-0.6449-0.06880.25890.01650.3770.33650.2345-0.10251.09590.1472-0.040811.2066-12.30891.7446
291.1219-0.0759-0.33760.52290.2370.19150.09361.38721.0264-0.3144-0.10910.0117-0.2253-0.34670.12850.17670.079-0.11440.80940.53630.631318.5925-1.48479.1067
305.4012-2.3527-2.79474.4585-3.07726.82330.34260.98560.93510.0319-0.4273-0.1968-0.37040.54780.12480.27480.0180.0430.92360.27680.437226.9403-10.647710.4055
314.1358-0.5824-1.01460.6939-0.6551.29120.07791.42680.0954-0.21960.00330.170.0711-0.12420.00280.39060.21310.06051.25440.16240.298822.644-16.85040.9121
322.33161.003-1.19421.6657-1.49752.3074-0.03481.3830.3989-0.58650.12260.13790.2216-0.7618-0.16180.45980.10370.12961.2090.48010.491720.6137-6.27711.3371
330.99471.09081.01451.55580.57381.8448-0.310.03431.18440.2061-0.236-0.7515-0.61120.67840.57170.3933-0.2284-0.16360.66280.27311.403428.93854.123422.2966
343.2523-2.1808-0.44813.12392.50965.3551-0.3906-0.39931.37940.69670.5392-0.90810.07910.7514-0.25850.5107-0.0665-0.37370.3151-0.06830.787824.4705-2.797729.8106
355.69760.33672.52244.22572.1562.24-0.081-0.12710.48540.9775-0.2536-0.53680.0939-0.13950.36680.6068-0.0154-0.15250.30980.06350.226715.6785-11.589827.9848
362.49-1.72441.79856.7366-1.8632.6504-0.1780.30670.81580.2067-0.2933-0.4189-0.34680.57670.43740.271-0.0725-0.08740.28120.16660.38616.0226-5.313721.3062
374.94014.8220.53714.70790.52410.0582-0.34340.4041.03270.2654-0.371-1.7341-0.53580.78310.76830.6585-0.0774-0.35920.41980.30251.479619.31017.811523.0556
386.13870.09-1.74892.0773-2.6383.78530.30260.98832.025-0.2466-0.3604-0.5739-0.30730.24050.01740.520.07380.2740.90250.76291.905824.49088.012613.2216
391.55061.53720.10712.6624-1.76953.09810.09441.59540.7537-0.8291-0.195-0.7050.05250.17310.05510.44520.10330.31311.15730.4880.750827.7026-4.24462.888
405.23632.7304-0.87488.3905-1.78441.6176-0.26241.5699-0.0185-0.85990.7277-0.04030.0322-0.9214-0.42210.44730.04860.02181.47740.24090.425229.9016-18.54392.5914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:25)
2X-RAY DIFFRACTION2(chain A and resid 26:40)
3X-RAY DIFFRACTION3(chain A and resid 41:45)
4X-RAY DIFFRACTION4(chain A and resid 46:55)
5X-RAY DIFFRACTION5(chain A and resid 56:61)
6X-RAY DIFFRACTION6(chain A and resid 62:79)
7X-RAY DIFFRACTION7(chain A and resid 80:97)
8X-RAY DIFFRACTION8(chain A and resid 98:102)
9X-RAY DIFFRACTION9(chain A and resid 103:113)
10X-RAY DIFFRACTION10(chain A and resid 114:118)
11X-RAY DIFFRACTION11(chain A and resid 119:136)
12X-RAY DIFFRACTION12(chain A and resid 137:141)
13X-RAY DIFFRACTION13(chain A and resid 142:152)
14X-RAY DIFFRACTION14(chain A and resid 153:164)
15X-RAY DIFFRACTION15(chain A and resid 165:178)
16X-RAY DIFFRACTION16(chain A and resid 179:187)
17X-RAY DIFFRACTION17(chain A and resid 188:194)
18X-RAY DIFFRACTION18(chain A and resid 195:210)
19X-RAY DIFFRACTION19(chain A and resid 211:225)
20X-RAY DIFFRACTION20(chain A and resid 226:234)
21X-RAY DIFFRACTION21(chain B and resid 7:17)
22X-RAY DIFFRACTION22(chain B and resid 18:39)
23X-RAY DIFFRACTION23(chain B and resid 40:52)
24X-RAY DIFFRACTION24(chain B and resid 53:61)
25X-RAY DIFFRACTION25(chain B and resid 62:76)
26X-RAY DIFFRACTION26(chain B and resid 77:87)
27X-RAY DIFFRACTION27(chain B and resid 88:98)
28X-RAY DIFFRACTION28(chain B and resid 99:114)
29X-RAY DIFFRACTION29(chain B and resid 115:126)
30X-RAY DIFFRACTION30(chain B and resid 127:134)
31X-RAY DIFFRACTION31(chain B and resid 135:141)
32X-RAY DIFFRACTION32(chain B and resid 142:154)
33X-RAY DIFFRACTION33(chain B and resid 155:166)
34X-RAY DIFFRACTION34(chain B and resid 175:188)
35X-RAY DIFFRACTION35(chain B and resid 189:196)
36X-RAY DIFFRACTION36(chain B and resid 197:208)
37X-RAY DIFFRACTION37(chain B and resid 209:214)
38X-RAY DIFFRACTION38(chain B and resid 215:222)
39X-RAY DIFFRACTION39(chain B and resid 223:230)
40X-RAY DIFFRACTION40(chain B and resid 231:236)

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