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- PDB-3mxm: TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant -

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Basic information

Entry
Database: PDB / ID: 3mxm
TitleTREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant
Components
  • DNA (5'-D(*GP*AP*CP*G)-3')
  • Three prime repair exonuclease 1
KeywordsHYDROLASE/DNA / RNase H-like fold / Polyproline type II helix / HYDROLASE-DNA complex
Function / homology
Function and homology information


immune response in brain or nervous system / T cell antigen processing and presentation / immune complex formation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition ...immune response in brain or nervous system / T cell antigen processing and presentation / immune complex formation / organ or tissue specific immune response / adenyl deoxyribonucleotide binding / activation of immune response / DNA synthesis involved in UV-damage excision repair / atrial cardiac muscle tissue development / lymphoid progenitor cell differentiation / retrotransposition / MutSalpha complex binding / DNA exonuclease activity / regulation of catalytic activity / DNA modification / regulation of immunoglobulin production / cellular response to hydroxyurea / regulation of lipid biosynthetic process / oligosaccharyltransferase complex / regulation of lysosome organization / regulation of cellular respiration / regulation of fatty acid metabolic process / regulation of protein complex stability / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / regulation of type I interferon production / inflammatory response to antigenic stimulus / regulation of tumor necrosis factor production / regulation of T cell activation / 3'-5'-DNA exonuclease activity / heart process / blood vessel development / macrophage activation involved in immune response / MutLalpha complex binding / glycoprotein biosynthetic process / DNA catabolic process / apoptotic cell clearance / negative regulation of type I interferon-mediated signaling pathway / regulation of glycolytic process / DNA binding, bending / DNA metabolic process / type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / WW domain binding / regulation of innate immune response / cellular response to type I interferon / negative regulation of cGAS/STING signaling pathway / nuclear replication fork / response to UV / heart morphogenesis / determination of adult lifespan / cellular response to interferon-beta / DNA damage checkpoint signaling / kidney development / mitotic G1 DNA damage checkpoint signaling / 3'-5' exonuclease activity / negative regulation of innate immune response / cellular response to gamma radiation / generation of precursor metabolites and energy / establishment of protein localization / cellular response to reactive oxygen species / protein-DNA complex / cellular response to UV / regulation of gene expression / single-stranded DNA binding / 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 / 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
IODIDE ION / DNA / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBailey, S.L. / Hollis, T.
CitationJournal: To be Published
Title: X-ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants
Authors: Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_auth_seq_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_conn.ptnr2_label_seq_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: DNA (5'-D(*GP*AP*CP*G)-3')
D: DNA (5'-D(*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,79520
Polymers55,1124
Non-polymers1,68316
Water9,710539
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Three prime repair exonuclease 1
C: DNA (5'-D(*GP*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,79520
Polymers55,1124
Non-polymers1,68316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area5320 Å2
ΔGint-63 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.468, 86.026, 92.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26339.918 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242 / Mutation: V201D
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 DNA (5'-D(*GP*AP*CP*G)-3')


Mass: 1215.843 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 3350 0.1 M NaI 5% 1,4-butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→47 Å / Num. obs: 57078 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Biso Wilson estimate: 17.58 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.62 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.4 / % possible all: 91.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_113)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→18.706 Å / SU ML: 0.2 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2870 5.08 %Random
Rwork0.1715 ---
obs0.1731 56543 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.851 Å2 / ksol: 0.392 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0014 Å20 Å2-0 Å2
2--0.6829 Å20 Å2
3----0.6843 Å2
Refinement stepCycle: LAST / Resolution: 1.75→18.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 162 16 539 4184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063735
X-RAY DIFFRACTIONf_angle_d1.1125123
X-RAY DIFFRACTIONf_dihedral_angle_d18.1951393
X-RAY DIFFRACTIONf_chiral_restr0.076580
X-RAY DIFFRACTIONf_plane_restr0.005642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.81250.24042660.19694875X-RAY DIFFRACTION91
1.8125-1.8850.21352750.18225339X-RAY DIFFRACTION99
1.885-1.97070.23482800.18145361X-RAY DIFFRACTION99
1.9707-2.07450.21673100.17435337X-RAY DIFFRACTION99
2.0745-2.20430.20582970.16275398X-RAY DIFFRACTION100
2.2043-2.37420.20412820.15865391X-RAY DIFFRACTION99
2.3742-2.61250.19973050.16235401X-RAY DIFFRACTION99
2.6125-2.98920.20042800.16545457X-RAY DIFFRACTION100
2.9892-3.76110.16692930.16085509X-RAY DIFFRACTION100
3.7611-18.70750.18352820.16145605X-RAY DIFFRACTION98
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)
10.7714-0.1550.04451.0386-0.25380.0315-0.059-0.01340.1310.11070.0535-0.0614-0.0376-0.00950.01990.0791-0.0011-0.01870.0810.00360.086417.499320.9162-4.7849
20.5288-0.68990.42421.0002-0.57550.33170.53730.43350.2488-0.352-0.26960.2533-0.36310.0775-0.21810.29550.19650.01560.46660.0840.183717.28122.7741-26.8404
31.45620.54060.06251.01640.70850.57650.34380.5845-0.0962-0.2502-0.00620.112-0.01970.3559-0.26230.19330.104-0.01660.26170.00310.12225.980621.4646-26.7752
40.1987-0.3552-0.08340.66710.16520.632-0.0036-0.0103-0.00460.0220.05010.06990.0173-0.045-0.03420.08040.0061-0.00280.10880.00470.078510.333110.699-1.5123
50.2979-0.3551-0.38410.73130.24160.5807-0.1076-0.00780.00180.09730.1103-0.16980.08920.0206-0.01920.0960.0065-0.02670.0981-0.01120.099722.28419.39690.2995
60.4364-0.06650.02320.2567-0.05771.0448-0.0423-0.03810.16740.050.0366-0.1017-0.04570.06850.00710.08790.0102-0.01720.0798-0.01870.13318.138925.4557-2.6406
79.52881.1349-5.59368.42660.46863.4935-0.0147-0.24510.7584-0.1441-0.48031.0908-0.0012-0.31110.42020.22410.04740.00410.2416-0.05940.46151.679738.8239-15.7752
80.646-0.13530.2970.2070.17491.1820.05940.02040.0943-0.0079-0.03880.03640.1088-0.0913-0.01940.09190.0113-0.00890.11640.01670.11491.843424.1381-15.436
90.6158-0.11870.03180.9759-0.62790.6520.07010.03730.15040.0591-0.00380.159-0.0483-0.0177-0.05210.08470.0164-0.00520.09350.00970.1111.029421.1977-14.8593
100.8243-0.45-0.04020.39050.08740.3155-0.0076-0.0110.31330.05020.0253-0.1090.04050.0488-0.01160.1017-0.0165-0.02320.0751-0.00130.179320.621730.3732-3.549
110.58680.09980.28580.45620.38710.67660.03950.0365-0.1050.01550.0056-0.04390.16430.1198-0.05040.11830.0245-0.00770.0997-0.00610.100122.258-5.3159-11.456
120.96270.6037-0.43060.4858-0.59561.1005-0.17970.34870.0329-0.02230.14610.10880.422-0.82730.07510.3351-0.24760.07430.683-0.1980.30561.7691-7.9583-5.9751
130.42830.21140.64790.3340.51481.143-0.0948-0.78250.59080.1452-0.11930.1672-0.0999-0.42020.20620.1249-0.0173-0.02550.2543-0.14130.2453-1.5458-6.1673-15.9183
140.4162-0.08180.26570.4450.1010.20640.00860.1860.0258-0.1663-0.009-0.01510.03560.12220.0040.1265-0.00130.00290.155-0.01020.076523.4034.8932-19.9446
150.2220.01760.52891.1931-0.32221.60070.09330.22290.04360.07380.0884-0.1721-0.21640.1511-0.1210.09050.00940.02650.1496-0.00120.163732.21649.3335-14.4236
160.4471-0.1534-0.00970.17070.07190.73040.0542-0.0129-0.18330.10720.0316-0.07290.24680.0893-0.06850.15240.0113-0.00980.1006-0.01460.130522.5491-4.5277-4.8991
170.52620.3494-0.08250.8380.28010.2443-0.04830.1768-0.124-0.05890.128-0.10510.12910.1109-0.0270.15930.03920.00650.1425-0.03440.126531.7723-6.4728-15.6723
180.7197-0.416-0.06770.59650.28551.0695-0.00760.1542-0.4051-0.06360.0639-0.0780.23030.1092-0.09020.1870.0012-0.02570.0788-0.03240.163619.5216-13.4234-12.715
190.71680.45830.14470.32240.18810.2931-0.01370.09690.0965-0.13990.04710.11280.10720.0014-0.01390.1394-0.0078-0.03210.1107-0.03840.12759.5502-5.2669-19.7296
201.64920.102-0.40020.1270.24961.3886-0.0265-0.0317-0.36380.0339-0.0121-0.1150.46160.030.03710.23470.0368-0.02230.0976-0.01480.202522.501-14.4755-9.0011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:41)
2X-RAY DIFFRACTION2(chain A and resid 42:51)
3X-RAY DIFFRACTION3(chain A and resid 52:59)
4X-RAY DIFFRACTION4(chain A and resid 60:90)
5X-RAY DIFFRACTION5(chain A and resid 91:117)
6X-RAY DIFFRACTION6(chain A and resid 118:165)
7X-RAY DIFFRACTION7(chain A and resid 166:174)
8X-RAY DIFFRACTION8(chain A and resid 175:193)
9X-RAY DIFFRACTION9(chain A and resid 194:215)
10X-RAY DIFFRACTION10(chain A and resid 216:234)
11X-RAY DIFFRACTION11(chain B and resid 6:42)
12X-RAY DIFFRACTION12(chain B and resid 43:51)
13X-RAY DIFFRACTION13(chain B and resid 52:59)
14X-RAY DIFFRACTION14(chain B and resid 60:90)
15X-RAY DIFFRACTION15(chain B and resid 91:108)
16X-RAY DIFFRACTION16(chain B and resid 109:127)
17X-RAY DIFFRACTION17(chain B and resid 128:140)
18X-RAY DIFFRACTION18(chain B and resid 141:177)
19X-RAY DIFFRACTION19(chain B and resid 178:211)
20X-RAY DIFFRACTION20(chain B and resid 212:234)

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