- EMDB-21046: Cryo-EM map of the core of human histone pre-mRNA cleavage comple... -
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Basic information
Entry
Database: EMDB / ID: EMD-21046
Title
Cryo-EM map of the core of human histone pre-mRNA cleavage complex (CPSF73-CPSF100-Symplekin)
Map data
The core of human histone cleavage complex CPSF73-CPSF100-Symplekin
Sample
Complex: The core of human histone cleavage complex CPSF73-CPSF100-Symplekin
Function / homology
Function and homology information
histone mRNA metabolic process / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / 5'-3' RNA exonuclease activity / nuclear stress granule / Processing of Intronless Pre-mRNAs / regulation of chromatin organization / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...histone mRNA metabolic process / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / 5'-3' RNA exonuclease activity / nuclear stress granule / Processing of Intronless Pre-mRNAs / regulation of chromatin organization / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 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 / mRNA 3'-end processing / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / mRNA 3'-end processing / pICln-Sm protein complex / Transport of Mature mRNA Derived from an Intronless Transcript / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / : / termination of RNA polymerase II transcription / precatalytic spliceosome / 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 / spliceosomal snRNP assembly / Cajal body / U4/U6 x U5 tri-snRNP complex / RNA endonuclease activity / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / negative regulation of protein binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / postsynapse / cytoskeleton / nuclear body / cell adhesion / ribonucleoprotein complex / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Symplekin/Pta1 ...Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term / CPSF73-100_C / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Armadillo-like helical / Armadillo-type fold Similarity search - Domain/homology
Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U7 snRNA-associated Sm-like protein LSm11 / Symplekin / U7 snRNA-associated Sm-like protein LSm10 / Cleavage and polyadenylation specificity factor subunit 2 / Cleavage and polyadenylation specificity factor subunit 3 Similarity search - Component
Biological species
Homo sapiens (human)
Method
single particle reconstruction / cryo EM / Resolution: 4.1 Å
National Institutes of Health/National Institute of General Medical Sciences
R35GM118093
United States
National Institutes of Health/National Institute of General Medical Sciences
R01GM029832
United States
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
Deposition
Nov 28, 2019
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Header (metadata) release
Mar 4, 2020
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Map release
Mar 4, 2020
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Update
Mar 4, 2020
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Current status
Mar 4, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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