+Open data
-Basic information
Entry | Database: PDB / ID: 7afs | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of Artemis variant D37A | ||||||
Components | Protein artemis | ||||||
Keywords | HYDROLASE / Artemis / SNM1C / DCLRE1C / Nuclease | ||||||
Function / homology | Function and homology information single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / 5'-3' exonuclease activity / V(D)J recombination / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) ...single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / 5'-3' exonuclease activity / V(D)J recombination / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / endonuclease activity / adaptive immune response / damaged DNA binding / Hydrolases; Acting on ester bonds / Golgi apparatus / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Yosaatmadja, Y. / Goubin, S. / Newman, J.A. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Gileadi, O. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition. Authors: Yosaatmadja, Y. / Baddock, H.T. / Newman, J.A. / Bielinski, M. / Gavard, A.E. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Schofield, C.J. / McHugh, P.J. / Gileadi, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7afs.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7afs.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 7afs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/7afs ftp://data.pdbj.org/pub/pdb/validation_reports/af/7afs | HTTPS FTP |
---|
-Related structure data
Related structure data | 6tt5SC 7absC 7af1C 7afuC 7agiC 7apvC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41729.062 Da / Num. of mol.: 1 / Mutation: D37A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1C, ARTEMIS, ASCID, SCIDA, SNM1C / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NI / | ||||
#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.09 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Ammonium Acetate, 0.1 M Bis-TRIS pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 17, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.7→47.66 Å / Num. obs: 33287 / % possible obs: 97.3 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.7 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.7 %
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TT5 Resolution: 1.7→47.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.1314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.51 Å2 / Biso mean: 25.925 Å2 / Biso min: 14.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→47.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|