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- PDB-3nyb: Structure and function of the polymerase core of TRAMP, a RNA sur... -
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Basic information
Entry | Database: PDB / ID: 3nyb | ||||||
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Title | Structure and function of the polymerase core of TRAMP, a RNA surveillance complex | ||||||
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![]() | TRANSFERASE/RNA BINDING PROTEIN / polyA RNA polymerase / zinc knuckle protein / RNA surveillance / Mtr4p binds to Trf4p/Air2p heterodimer / TRANSFERASE-RNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / RNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / meiotic DNA double-strand break formation / TRAMP-dependent tRNA surveillance pathway ...polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / RNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / meiotic DNA double-strand break formation / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / histone mRNA catabolic process / tRNA modification / negative regulation of DNA recombination / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 5'-deoxyribose-5-phosphate lyase activity / localization / base-excision repair / protein-macromolecule adaptor activity / molecular adaptor activity / cell division / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reinisch, K.M. / Hamill, S. | ||||||
![]() | ![]() Title: Structure and function of the polymerase core of TRAMP, a RNA surveillance complex. Authors: Hamill, S. / Wolin, S.L. / Reinisch, K.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.3 KB | Display | ![]() |
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PDB format | ![]() | 135.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 23.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36459.453 Da / Num. of mol.: 1 Fragment: central and catalytic domains of Trf4p (UNP residues 161-481) Mutation: D293A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PAP2, TRF4, YOL115W, O0716, HRC584 / Production host: ![]() ![]() References: UniProt: P53632, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||
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#2: Protein | Mass: 9399.759 Da / Num. of mol.: 1 Fragment: fourth and fifth zinc knuckles of Air2p (UNP residues 118-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: AIR2, YDL175C / Production host: ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2009 | |||||||||||||||
Radiation | Monochromator: cryogenically cooled Si double crystal (111) monochromator Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.28215 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.6→25 Å / Num. all: 16163 / Num. obs: 16163 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.077 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.544 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7007→24.656 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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