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Open data
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Basic information
Entry | Database: PDB / ID: 6qw6 | |||||||||
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Title | Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution. | |||||||||
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![]() | SPLICING / RNP complex / RNA / protein / spliceosome | |||||||||
Function / homology | ![]() Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / U4atac snRNA binding ...Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA binding / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / P-body assembly / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / U3 snoRNA binding / U1 snRNP / tRNA processing / Cajal body / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / negative regulation of mRNA splicing, via spliceosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / maturation of SSU-rRNA / small-subunit processome / response to bacterium / spliceosomal complex / P-body / small GTPase binding / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / ATPase binding / ribosomal small subunit biogenesis Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | |||||||||
![]() | Charenton, C. / Wilkinson, M.E. / Nagai, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of 5' splice site transfer for human spliceosome activation. Authors: Clément Charenton / Max E Wilkinson / Kiyoshi Nagai / ![]() Abstract: The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 ...The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4658MC ![]() 4665C ![]() 4672C ![]() 4673C ![]() 4674C ![]() 4675C ![]() 4676C ![]() 4686C ![]() 4687C ![]() 4688C ![]() 4689C ![]() 4690C ![]() 6qx9C M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Dataset 1 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #2: Dataset 2 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #3: Dataset 3 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #4: Dataset 4 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #5: Dataset 5 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #6: Selected U4/U6.U5 tri-snRNP particles after Bayesian polishing [picked particles - single frame - processed] Data #7: Crude shifted preB particles [picked particles - single frame - unprocessed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 9 types, 10 molecules X4D4b5b5A5C5D5J5XR
#1: Protein | Mass: 18915.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||
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#9: Protein | Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||
#10: Protein | Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | | Mass: 271508.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | | Mass: 95836.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | | Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | | Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | | Mass: 95785.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #30: Protein | | Mass: 50477.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 3 types, 3 molecules 456
#2: RNA chain | Mass: 46997.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#14: RNA chain | Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: RNA chain | Mass: 28342.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules 4151425243534e5e4f5f4g5g
#3: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules 4A4B4C
#6: Protein | Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules 5B5O
#16: Protein | Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#20: Protein | Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules 62636465666768
#23: Protein | Mass: 10847.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#24: Protein | Mass: 11859.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 15375.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 9945.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 9139.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 11617.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#29: Protein | Mass: 10410.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-U4/U6.U5 tri-snRNP-associated protein ... , 2 types, 2 molecules SU
#31: Protein | Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#32: Protein | Mass: 64408.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 4 molecules ![](data/chem/img/IHP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
#33: Chemical | ChemComp-IHP / |
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#34: Chemical | ChemComp-MG / |
#35: Chemical | ChemComp-GTP / |
#36: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 1.7 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Wait 30s, blot for 2s to 3s. |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1147653 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 585488 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT |