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Yorodumi- PDB-6am0: Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6am0 | |||||||||
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Title | Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap substrate analog | |||||||||
Components |
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Keywords | TRANSLATION / mRNA decay / decapping / Nudix / nucleotide analog | |||||||||
Function / homology | Function and homology information deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / enzyme activator activity / P-body / manganese ion binding / mRNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | Kluyveromyces lactis (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | |||||||||
Authors | Mugridge, J.S. / Gross, J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Authors: Mugridge, J.S. / Tibble, R.W. / Ziemniak, M. / Jemielity, J. / Gross, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6am0.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6am0.ent.gz | 192.9 KB | Display | PDB format |
PDBx/mmJSON format | 6am0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/6am0 ftp://data.pdbj.org/pub/pdb/validation_reports/am/6am0 | HTTPS FTP |
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-Related structure data
Related structure data | 5lopS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules AEBFDH
#1: Protein | Mass: 31804.855 Da / Num. of mol.: 2 / Fragment: unp residues 1-275 / Mutation: E152Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_F23980g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q6CIU1 #2: Protein | Mass: 22073.959 Da / Num. of mol.: 2 / Fragment: unp residues 1-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E01827g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPV9 #4: Protein | Mass: 7331.633 Da / Num. of mol.: 2 / Fragment: unp residues 1-66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_A11308g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*DE3 / References: UniProt: Q6CX48 |
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-Protein/peptide , 1 types, 2 molecules CG
#3: Protein/peptide | Mass: 2755.126 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) References: UniProt: Q6CYC5 |
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-Non-polymers , 2 types, 3 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58 % / Description: rhombohedral blocks, ~40-80 microns. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution: 4mg/mL Kl Dcp1/Dcp2/Edc3, 1mM Edc1 peptide, 6mM substrate analog, 10mM magnsium chloride. Well solution: 0.22M magnesium chloride, 0.03M EDTA, 8% PEG 8000. Procedure: 250nL ...Details: Protein solution: 4mg/mL Kl Dcp1/Dcp2/Edc3, 1mM Edc1 peptide, 6mM substrate analog, 10mM magnsium chloride. Well solution: 0.22M magnesium chloride, 0.03M EDTA, 8% PEG 8000. Procedure: 250nL protein solution + 250nL well solution + 50nL 1:10000 seed stock. Set up at RT, grow crystals at 4C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 68126 / % possible obs: 98.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.82 |
Reflection shell | Resolution: 2.84→3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LOP Resolution: 2.84→45.96 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→45.96 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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