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Yorodumi- PDB-6v4x: Cryo-EM structure of an active human histone pre-mRNA 3'-end proc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v4x | |||||||||
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Title | Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 Angstrom resolution | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / endonuclease / active CPSF73 / U7 snRNP / 3'-end processing / RIBONUCLEASE / RNA BINDING PROTEIN-RNA complex | |||||||||
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 / mRNA cleavage and polyadenylation specificity factor complex / U2 snRNP binding / U7 snRNA 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 / mRNA cleavage and polyadenylation specificity factor complex / 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 / Transport of Mature mRNA Derived from an Intronless Transcript / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / pICln-Sm protein complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / mRNA 3'-end processing / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / Cajal body / U2-type prespliceosome / termination of RNA polymerase II transcription / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / bicellular tight junction / U5 snRNP / 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 / 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 | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Sun, Y. / Zhang, Y. / Walz, T. / Tong, L. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v4x.cif.gz | 412.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4x.ent.gz | 306.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v4x_validation.pdf.gz | 995.7 KB | Display | wwPDB validaton report |
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Full document | 6v4x_full_validation.pdf.gz | 1022.5 KB | Display | |
Data in XML | 6v4x_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 6v4x_validation.cif.gz | 87.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4x ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4x | HTTPS FTP |
-Related structure data
Related structure data | 21050MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Small nuclear ribonucleoprotein ... , 4 types, 4 molecules AFEG
#1: Protein | Mass: 16111.671 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62318 |
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#3: Protein | Mass: 9734.171 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPF, PBSCF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62306 |
#4: Protein | Mass: 10817.601 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62304 |
#5: Protein | Mass: 9579.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPG, PBSCG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62308 |
-Protein , 2 types, 2 molecules BJ
#2: Protein | Mass: 10911.931 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPB, COD, SNRPB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14678 |
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#10: Protein | Mass: 120355.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYMPK, SPK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92797 |
-U7 snRNA-associated Sm-like protein ... , 2 types, 2 molecules CD
#6: Protein | Mass: 14102.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSM10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q969L4 |
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#7: Protein | Mass: 28609.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LSM11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P83369 |
-Cleavage and polyadenylation specificity factor subunit ... , 2 types, 2 molecules HI
#8: Protein | Mass: 77580.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF3, CPSF73 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9UKF6, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#9: Protein | Mass: 88597.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF2, CPSF100, KIAA1367 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9P2I0 |
-RNA chain , 2 types, 2 molecules ZY
#11: RNA chain | Mass: 19097.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1633547 |
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#12: RNA chain | Mass: 16626.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) |
-Non-polymers , 1 types, 2 molecules
#13: Chemical |
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-Details
Has ligand of interest | Y |
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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: The core of metazoan replication-dependent histone pre-mRNA 3'-end processing machinery Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 100 mM / Name: sodium chloride / Formula: NaCl |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 2800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm | |||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | |||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325282 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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