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Yorodumi- PDB-2nn6: Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp4... -
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-Basic information
Entry | Database: PDB / ID: 2nn6 | ||||||
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Title | Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40 | ||||||
Components |
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Keywords | HYDROLASE/TRANSFERASE / RNA / exosome / PM/Scl / exoribonuclease / phosphorolytic / ribonuclease / HYDROLASE-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information : / mRNA 3'-UTR AU-rich region binding => GO:0035925 / : / DNA deamination / nucleolar exosome (RNase complex) / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway ...: / mRNA 3'-UTR AU-rich region binding => GO:0035925 / : / DNA deamination / nucleolar exosome (RNase complex) / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / histone mRNA catabolic process / nuclear mRNA surveillance / positive regulation of isotype switching / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / RNA catabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / KSRP (KHSRP) binds and destabilizes mRNA / nuclear chromosome / maturation of 5.8S rRNA / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / regulation of mRNA stability / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / 3'-5'-RNA exonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / immune response / intracellular membrane-bounded organelle / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.35 Å | ||||||
Authors | Lima, C.D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Reconstitution, activities, and structure of the eukaryotic RNA exosome. Authors: Liu, Q. / Greimann, J.C. / Lima, C.D. | ||||||
History |
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Remark 999 | SEQUENCE IN THE C-TERMINAL REGION OF CHAIN "A", 303-456, ONLY THIRTY EIGHT RESIDUES WERE VISIBLE ... SEQUENCE IN THE C-TERMINAL REGION OF CHAIN "A", 303-456, ONLY THIRTY EIGHT RESIDUES WERE VISIBLE IN ELECTRON DENSITY. THE SEQUENCE NUMBERING 412-449 OF THESE 38 RESIDUES IN CHAIN A IS RANDOM, AND THESE RESIDUES ARE ASSIGNED AS "UNK" (UNKNOWN AMINO ACIDS). THE SEQUENCE ALIGNMENT IS UNKNOWN IN THIS REGION. THE SEQUENCE IN THIS DISORDERED REGION (RESIDUES 303-456) IS: IDTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGD LEDSEKEDDEGGGDQAIILDGIKMDTGVEVSDIGSQELGFHHVGQTG LEFLTSDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQEKAPSK KPVKRRKKKRAAN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nn6.cif.gz | 442.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nn6.ent.gz | 349.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nn6_validation.pdf.gz | 540.4 KB | Display | wwPDB validaton report |
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Full document | 2nn6_full_validation.pdf.gz | 896.9 KB | Display | |
Data in XML | 2nn6_validation.xml.gz | 125.9 KB | Display | |
Data in CIF | 2nn6_validation.cif.gz | 167.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nn6 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nn6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules AFI
#1: Protein | Mass: 39405.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: PMSCL1 / Plasmid: pETDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL / References: UniProt: Q86Y41, UniProt: Q06265*PLUS |
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#6: Protein | Mass: 28267.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC6 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q5RKV6 |
#9: Protein | Mass: 23097.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC1, CSL4 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q9Y3B2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
-Exosome complex exonuclease ... , 6 types, 6 molecules BCDEGH
#2: Protein | Mass: 26831.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC4, RRP41, SKI6 / Plasmid: pETDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q9NPD3, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#3: Protein | Mass: 30285.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC8, OIP2, RRP43 / Plasmid: pSMT3 (Smt3 fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q96B26, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#4: Protein | Mass: 25480.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC5, CML28, RRP46 / Plasmid: pSMT3 (Smt3-fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q9NQT4, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#5: Protein | Mass: 33479.121 Da / Num. of mol.: 1 / Mutation: L274V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC7, KIAA0116, RRP42 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star References: UniProt: Q15024, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#7: Protein | Mass: 31227.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC3, RRP40 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q9NQT5, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
#8: Protein | Mass: 34590.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: placental cDNA (Ambion, Inc) / Gene: EXOSC2, RRP4 / Plasmid: pRSFDuet-1 (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL References: UniProt: Q13868, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 4.5-8% w/v PEG4000, 0.1M Sodium citrate, 1 mM TCEP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9809 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→35 Å / Num. all: 69964 / Num. obs: 69964 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6999 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.35→14.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 59512279.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED CNS version 1.2 grid search used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5031 Å2 / ksol: 0.26 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.35→14.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.35→3.47 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
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Xplor file |
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