+Open data
-Basic information
Entry | Database: PDB / ID: 7a9w | ||||||||||||||||||
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Title | Structure of yeast Rmd9p in complex with 20nt target RNA | ||||||||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN / Mitochondria / Translation / Transcription / Degradation / Ribosome | ||||||||||||||||||
Function / homology | Function and homology information 3'-UTR-mediated mRNA stabilization / sporulation resulting in formation of a cellular spore / regulation of mRNA stability / mRNA 3'-UTR binding / translational initiation / aerobic respiration / mitochondrial inner membrane / mRNA binding / mitochondrion Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||||||||||||||
Authors | Hillen, H.S. / Markov, D.A. / Ireneusz, W.D. / Hofmann, K.B. / Cowan, A.T. / Jones, J.L. / Temiakov, D. / Cramer, P. / Anikin, M. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs. Authors: Hillen, H.S. / Markov, D.A. / Wojtas, I.D. / Hofmann, K.B. / Lidschreiber, M. / Cowan, A.T. / Jones, J.L. / Temiakov, D. / Cramer, P. / Anikin, M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a9w.cif.gz | 291.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a9w.ent.gz | 203.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a9w_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 7a9w_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 7a9w_validation.xml.gz | 20 KB | Display | |
Data in CIF | 7a9w_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/7a9w ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a9w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70264.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RMD9, YGL107C, G3075 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: P53140 |
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#2: RNA chain | Mass: 6306.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 Details: Na-Cacodylate, NaCl, LiSO4, CaAcetate, MgCl2, PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→49.24 Å / Num. obs: 53148 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 77.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.16 |
Reflection shell | Resolution: 2.55→2.61 Å / Redundancy: 10.6 % / Rmerge(I) obs: 3.001 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 3965 / CC1/2: 0.373 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→49.24 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.9328 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→49.24 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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