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Yorodumi- PDB-6r5k: Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r5k | ||||||
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Title | Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / poly(A)-tail / mRNA / RNP / PABP / Pab1 / Pan2-Pan3 / Ccr4-Not / deadenylase / RRM / cryoEM | ||||||
Function / homology | Function and homology information regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / mRNA 3'-end processing / postreplication repair ...regulation of nuclear-transcribed mRNA poly(A) tail shortening / ribonuclease inhibitor activity / PAN complex / Deadenylation of mRNA / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / poly(A) binding / mRNA 3'-end processing / postreplication repair / poly(U) RNA binding / regulation of translational initiation / intracellular non-membrane-bounded organelle / mRNA transport / molecular condensate scaffold activity / mRNA 3'-UTR binding / promoter-specific chromatin binding / P-body / cytoplasmic stress granule / mRNA processing / nucleic acid binding / ribosome / protein kinase activity / ribonucleoprotein complex / DNA repair / mRNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||
Authors | Schaefer, I.B. / Conti, E. | ||||||
Citation | Journal: Cell / Year: 2019 Title: Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase. Authors: Ingmar B Schäfer / Masami Yamashita / Jan Michael Schuller / Steffen Schüssler / Peter Reichelt / Mike Strauss / Elena Conti / Abstract: The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs ...The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3' end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs' lifetime. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r5k.cif.gz | 607.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r5k.ent.gz | 456.6 KB | Display | PDB format |
PDBx/mmJSON format | 6r5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5k ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5k | HTTPS FTP |
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-Related structure data
Related structure data | 4728MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 4 molecules ADFH
#1: Protein | Mass: 127186.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PAN2, YGL094C / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53010, poly(A)-specific ribonuclease |
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#2: Protein | Mass: 64778.363 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PAB1, YER165W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04147 |
-PAN2-PAN3 deadenylation complex subunit ... , 2 types, 2 molecules NO
#4: Protein | Mass: 53218.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PAN3, ECM35, YKL025C / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36102 |
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#5: Protein | Mass: 77906.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: PAN3, ECM35, YKL025C / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P36102 |
-RNA chain / Non-polymers , 2 types, 3 molecules E
#3: RNA chain | Mass: 29583.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast) |
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#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.498 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 8 sec. / Electron dose: 51 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6463 |
Image scans | Sampling size: 5 µm / Movie frames/image: 40 / Used frames/image: 2-40 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2141230 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29165 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 45.7 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.8 Å / Stereochemistry target values: GeoStd + Monomer Library | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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