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Yorodumi- EMDB-21047: Cryo-EM map of the overall structure of human histone pre-mRNA 3'... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21047 | |||||||||
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Title | Cryo-EM map of the overall structure of human histone pre-mRNA 3'-end processing machinery | |||||||||
Map data | The overall structure of human histone pre-mRNA 3'-end processing machinery | |||||||||
Sample |
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Function / homology | Function and homology information histone mRNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / U2 snRNP binding / regulation of chromatin organization / U7 snRNA binding / histone pre-mRNA DCP binding / nuclear stress granule / Processing of Intronless Pre-mRNAs ...histone mRNA metabolic process / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA 3'-end processing by stem-loop binding and cleavage / 5'-3' RNA exonuclease activity / U2 snRNP binding / regulation of chromatin organization / U7 snRNA binding / histone pre-mRNA DCP binding / nuclear stress granule / Processing of Intronless Pre-mRNAs / U7 snRNP / mRNA cleavage and polyadenylation specificity factor complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / mRNA 3'-end processing / pICln-Sm protein complex / U1 snRNP binding / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / U2-type spliceosomal complex / telomerase RNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / : / termination of RNA polymerase II transcription / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / bicellular tight junction / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / Cajal body / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / negative regulation of protein binding / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / postsynapse / nuclear body / cytoskeleton / cell adhesion / ribonucleoprotein complex / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Sun Y / Zhang Y / Walz T / Tong L | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Science / Year: 2020 Title: Structure of an active human histone pre-mRNA 3'-end processing machinery. Authors: Yadong Sun / Yixiao Zhang / Wei Shen Aik / Xiao-Cui Yang / William F Marzluff / Thomas Walz / Zbigniew Dominski / Liang Tong / Abstract: The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with ...The 3'-end processing machinery for metazoan replication-dependent histone precursor messenger RNAs (pre-mRNAs) contains the U7 small nuclear ribonucleoprotein and shares the key cleavage module with the canonical cleavage and polyadenylation machinery. We reconstituted an active human histone pre-mRNA processing machinery using 13 recombinant proteins and two RNAs and determined its structure by cryo-electron microscopy. The overall structure is highly asymmetrical and resembles an amphora with one long handle. We captured the pre-mRNA in the active site of the endonuclease, the 73-kilodalton subunit of the cleavage and polyadenylation specificity factor, poised for cleavage. The endonuclease and the entire cleavage module undergo extensive rearrangements for activation, triggered through the recognition of the duplex between the authentic pre-mRNA and U7 small nuclear RNA (snRNA). Our study also has notable implications for understanding canonical and snRNA 3'-end processing. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21047.map.gz | 125 MB | EMDB map data format | |
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Header (meta data) | emd-21047-v30.xml emd-21047.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_21047.png | 72.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21047 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21047.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The overall structure of human histone pre-mRNA 3'-end processing machinery | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : The entire machinery of metazoan replication-dependent histone pr...
Entire | Name: The entire machinery of metazoan replication-dependent histone pre-mRNA 3'-end processing |
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Components |
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-Supramolecule #1: The entire machinery of metazoan replication-dependent histone pr...
Supramolecule | Name: The entire machinery of metazoan replication-dependent histone pre-mRNA 3'-end processing type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 100.0 mM / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride |
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.8 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 70.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 73.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 19315 |
Image recording ID | 1 |