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Yorodumi- PDB-7s7c: Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (subs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s7c | |||||||||
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Title | Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Helicase / ATPase / RNA / Exosome / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding ...snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / mRNA Splicing - Major Pathway / meiotic cell cycle / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / single-stranded RNA binding / nuclear body / RNA helicase / nuclear speck / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
Authors | Puno, M.R. / Lima, C.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2022 Title: Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Authors: M Rhyan Puno / Christopher D Lima / Abstract: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined ...RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s7c.cif.gz | 351.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s7c.ent.gz | 258.6 KB | Display | PDB format |
PDBx/mmJSON format | 7s7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s7c_validation.pdf.gz | 779.6 KB | Display | wwPDB validaton report |
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Full document | 7s7c_full_validation.pdf.gz | 799 KB | Display | |
Data in XML | 7s7c_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 7s7c_validation.cif.gz | 73.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/7s7c ftp://data.pdbj.org/pub/pdb/validation_reports/s7/7s7c | HTTPS FTP |
-Related structure data
Related structure data | 24883MC 7s7bC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 118224.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42285, RNA helicase #2: Protein | Mass: 69259.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZY4 #3: Protein | | Mass: 9462.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBM7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y580 #4: RNA chain | Mass: 9017.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #5: Chemical | ChemComp-ZN / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: 30 s wait time, blot for 2.5 s before plunging |
-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 |
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-Processing
EM software |
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Image processing | Details: 3 datasets collected using Gatan K2 Summit and Gatan K3 image detectors were used for the reconstructions. | |||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252638 Details: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map ...Details: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map with focused refinement maps of MTR4 core (3.5 Angstrom FSC=0.143), MTR4 core-ZCCHC8 PSP-RBM7-RNA (3.42 Angstrom, FSC=0.143), RBM7-RNA (3.94 Angstrom, FSC=0.143), MTR4-ZCCHC8 HD/KID (3.62 Angstrom, FSC=0.143), and MTR4 KOW-ZCCHC8 HD/KID (3.34 Angstrom, FSC=0.143) regions. Symmetry type: POINT |