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Yorodumi- EMDB-21050: Cryo-EM structure of an active human histone pre-mRNA 3'-end proc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21050 | |||||||||
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Title | Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution | |||||||||
Map data | active human histone pre-mRNA 3'-end processing machinery | |||||||||
Sample |
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Keywords | endonuclease / active CPSF73 / U7 snRNP / 3'-end processing / RIBONUCLEASE / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / regulation of chromatin organization / nuclear stress granule / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP ...cytoplasmic U snRNP body / mRNA 3'-end processing by stem-loop binding and cleavage / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / regulation of chromatin organization / nuclear stress granule / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 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 / U1 snRNP binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / pICln-Sm protein complex / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / Processing of Capped Intron-Containing Pre-mRNA / bicellular tight junction / U5 snRNP / positive regulation of G1/S transition of mitotic cell cycle / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / 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 / cytoskeleton / nuclear body / cell adhesion / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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_21050.map.gz | 133.2 MB | EMDB map data format | |
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Header (meta data) | emd-21050-v30.xml emd-21050.xml | 27.2 KB 27.2 KB | Display Display | EMDB header |
Images | emd_21050.png | 138.9 KB | ||
Filedesc metadata | emd-21050.cif.gz | 8.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21050 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21050 | HTTPS FTP |
-Validation report
Summary document | emd_21050_validation.pdf.gz | 543.6 KB | Display | EMDB validaton report |
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Full document | emd_21050_full_validation.pdf.gz | 543.2 KB | Display | |
Data in XML | emd_21050_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_21050_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21050 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21050 | HTTPS FTP |
-Related structure data
Related structure data | 6v4xMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_21050.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | active human histone pre-mRNA 3'-end processing machinery | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 core of metazoan replication-dependent histone pre-mRNA 3'-en...
+Supramolecule #1: The core of metazoan replication-dependent histone pre-mRNA 3'-en...
+Macromolecule #1: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #2: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #3: Small nuclear ribonucleoprotein F
+Macromolecule #4: Small nuclear ribonucleoprotein E
+Macromolecule #5: Small nuclear ribonucleoprotein G
+Macromolecule #6: U7 snRNA-associated Sm-like protein LSm10
+Macromolecule #7: U7 snRNA-associated Sm-like protein LSm11
+Macromolecule #8: Cleavage and polyadenylation specificity factor subunit 3
+Macromolecule #9: Cleavage and polyadenylation specificity factor subunit 2
+Macromolecule #10: Symplekin
+Macromolecule #11: U7 snRNA
+Macromolecule #12: modified H2a pre-mRNA
+Macromolecule #13: ZINC ION
-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: NaCl / 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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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |