+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14515 | |||||||||||||||
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Title | Human NEXT dimer in complex with the nuclear RNA exosome | |||||||||||||||
Map data | NEXT_S_with_nuclear_exosome_refine | |||||||||||||||
Sample |
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Keywords | HELICASE / ATPASE / RNA DEGRADATION / EXOSOME / RNA BINDING PROTEIN | |||||||||||||||
Function / homology | Function and homology information DNA deamination / nucleolar exosome (RNase complex) / : / snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome ...DNA deamination / nucleolar exosome (RNase complex) / : / snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / regulation of telomerase RNA localization to Cajal body / nuclear polyadenylation-dependent rRNA catabolic process / RNA exonuclease activity / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / 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 / snRNA binding / ATF4 activates genes in response to endoplasmic reticulum stress / rRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / histone mRNA catabolic process / nuclear mRNA surveillance / mRNA 3'-UTR AU-rich region binding / 7S RNA binding / isotype switching / telomerase RNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of alternative mRNA splicing, via spliceosome / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / negative regulation of telomere maintenance via telomerase / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding / catalytic step 2 spliceosome / transcription repressor complex / mRNA Splicing - Major Pathway / small-subunit processome / guanyl-nucleotide exchange factor activity / 14-3-3 protein binding / meiotic cell cycle / nuclear receptor binding / euchromatin / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / rRNA processing / transcription corepressor activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / positive regulation of cell growth / defense response to virus / endonuclease activity / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / single-stranded RNA binding / nuclear body / RNA helicase / nuclear speck / immune response / nucleotide binding / DNA repair / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA-templated transcription / apoptotic process / DNA damage response / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||||||||
Authors | Gerlach P / Lingaraju M / Salerno-Kochan A / Bonneau F / Basquin J / Conti E | |||||||||||||||
Funding support | Germany, European Union, 4 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome. Authors: Piotr Gerlach / William Garland / Mahesh Lingaraju / Anna Salerno-Kochan / Fabien Bonneau / Jérôme Basquin / Torben Heick Jensen / Elena Conti / Abstract: In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting ...In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3' end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14515.map.gz | 194.5 MB | EMDB map data format | |
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Header (meta data) | emd-14515-v30.xml emd-14515.xml | 38.7 KB 38.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14515_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_14515.png | 71.8 KB | ||
Masks | emd_14515_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-14515.cif.gz | 8.7 KB | ||
Others | emd_14515_additional_1.map.gz emd_14515_additional_2.map.gz emd_14515_half_map_1.map.gz emd_14515_half_map_2.map.gz | 229 MB 125.3 MB 194.1 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14515 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14515 | HTTPS FTP |
-Related structure data
Related structure data | 7z4yC 7z4zC 7z52C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14515.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | NEXT_S_with_nuclear_exosome_refine | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14515_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: NEXT S with nuclear exosome refine low pass 10
File | emd_14515_additional_1.map | ||||||||||||
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Annotation | NEXT_S_with_nuclear_exosome_refine_low_pass_10 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: NEXT S with nuclear exosome 3Dclass
File | emd_14515_additional_2.map | ||||||||||||
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Annotation | NEXT_S_with_nuclear_exosome_3Dclass | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: NEXT S with nuclear exosome half map 1
File | emd_14515_half_map_1.map | ||||||||||||
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Annotation | NEXT_S_with_nuclear_exosome_half_map_1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: NEXT S with nuclear exosome half map 2
File | emd_14515_half_map_2.map | ||||||||||||
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Annotation | NEXT_S_with_nuclear_exosome_half_map_2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human NEXT dimer in complex with the nuclear RNA exosome
+Supramolecule #1: Human NEXT dimer in complex with the nuclear RNA exosome
+Supramolecule #2: Human NEXT dimer in complex with the nuclear RNA exosome
+Supramolecule #3: RNA 5 prime hairpin U60
+Macromolecule #1: Exosome RNA helicase MTR4
+Macromolecule #2: Zinc finger CCHC domain-containing protein 8
+Macromolecule #3: RNA-binding protein 7
+Macromolecule #4: M-phase phosphoprotein 6
+Macromolecule #5: Nuclear nucleic acid-binding protein C1D
+Macromolecule #6: Exosome component 10
+Macromolecule #7: Exosome complex component CSL4
+Macromolecule #8: Exosome complex component RRP4
+Macromolecule #9: Exosome complex component RRP40
+Macromolecule #10: Exosome complex component RRP41
+Macromolecule #11: Exosome complex component RRP46
+Macromolecule #12: Exosome complex component MTR3
+Macromolecule #13: Exosome complex component RRP42
+Macromolecule #14: Exosome complex component RRP45
+Macromolecule #15: Exosome complex exonuclease RRP44
+Macromolecule #16: RNA 5 prime hairpin U60
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.1715 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |