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- PDB-2ioc: The crystal structure of TREX1 explains the 3' nucleotide specifi... -

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Basic information

Entry
Database: PDB / ID: 2ioc
TitleThe crystal structure of TREX1 explains the 3' nucleotide specificity and reveals a polyproline II helix for protein partenring
ComponentsThree prime repair exonuclease 1
KeywordsHYDROLASE / proline helix / nucleotide complex / DnaQ family
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 / regulation of fatty acid metabolic process / regulation of protein complex stability / cellular response to hydroxyurea / heart process / 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-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsde Silva, U. / Hollis, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals a Polyproline II Helix for Protein Partnering.
Authors: de Silva, U. / Choudhury, S. / Bailey, S.L. / Harvey, S. / Perrino, F.W. / Hollis, T.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7188
Polymers52,8362
Non-polymers8826
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-30 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.700, 119.700, 83.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsbiological assembly is the dimer in the asymmetric unit

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Components

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


Mass: 26417.750 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex1 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) / References: UniProt: Q91XB0, exodeoxyribonuclease III
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% PEG 3350, 100mM MES, 2mM MnCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 268K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→24.76 Å / Num. all: 25964 / Num. obs: 25938 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.62 % / Rmerge(I) obs: 0.125 / Χ2: 0.99 / Net I/σ(I): 7.7 / Scaling rejects: 2061
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.44 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.3 / Num. measured all: 26853 / Num. unique all: 4881 / Χ2: 1.2 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å38.67 Å
Translation2.5 Å38.67 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / FOM work R set: 0.845 / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1291 5 %random
Rwork0.198 ---
all-25964 --
obs-25938 99.9 %-
Solvent computationBsol: 41.78 Å2
Displacement parametersBiso mean: 22.365 Å2
Baniso -1Baniso -2Baniso -3
1--1.438 Å2-2.424 Å20 Å2
2---1.438 Å20 Å2
3---2.877 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 48 249 3687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.130.293530.23810051058
2.13-2.160.261540.2179511005
2.16-2.190.25550.2119821037
2.19-2.230.244600.2229981058
2.23-2.260.225450.2069821027
2.26-2.30.276530.2339901043
2.3-2.340.251550.2189981053
2.34-2.390.252550.2099901045
2.39-2.440.235520.2059581010
2.44-2.490.206490.2189871036
2.49-2.550.325390.22910081047
2.55-2.610.26510.22310091060
2.61-2.680.28570.2189721029
2.68-2.760.26540.2349851039
2.76-2.850.295550.2469781033
2.85-2.950.272590.2369691028
2.95-3.070.237430.2019971040
3.07-3.210.214520.1879741026
3.21-3.380.261530.2110081061
3.38-3.590.269580.2089611019
3.59-3.860.264580.1989901048
3.86-4.250.197570.1559791036
4.25-4.860.179430.15710071050
4.86-6.110.2430.1799741017
6.11-250.223380.189951033
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2amp_new.par
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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