+Open data
-Basic information
Entry | Database: PDB / ID: 7abi | ||||||
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Title | Human pre-Bact-2 spliceosome | ||||||
Components |
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Keywords | SPLICING / Complex / spliceosome / catalytic activation | ||||||
Function / homology | Function and homology information microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding ...microfibril / RES complex / somatic diversification of immunoglobulins / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / B-WICH complex / generation of catalytic spliceosome for first transesterification step / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / splicing factor binding / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / blastocyst formation / poly(A) binding / positive regulation of androgen receptor activity / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / transcription regulator inhibitor activity / U2 snRNP / nuclear vitamin D receptor binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / positive regulation of transcription by RNA polymerase III / Basigin interactions / U1 snRNP / RHOBTB1 GTPase cycle / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of RNA splicing / SMAD binding / mRNA 3'-splice site recognition / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNA binding / U5 snRNP / retinoic acid receptor signaling pathway / positive regulation of viral genome replication Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
Authors | Townsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Science / Year: 2020 Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA. | ||||||
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 | 7abi.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7abi.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 7abi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/7abi ftp://data.pdbj.org/pub/pdb/validation_reports/ab/7abi | HTTPS FTP |
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-Related structure data
Related structure data | 11697MC 7aavC 7abfC 7abgC 7abhC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10616 (Title: Cryo-EM dataset of human pre-Bact spliceosome / Data size: 584.5 Data #1: Motion-corrected micrographs (without dose-weighting) of human pre-Bact spliceosome [micrographs - single frame] Data #2: Motion-corrected micrographs (with dose-weighting) of human pre-Bact spliceosome [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules Ds
#1: Protein | Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7 |
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#13: Protein | Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase |
-Splicing factor 3B subunit ... , 6 types, 6 molecules EwxzuT
#2: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393 |
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#5: Protein | Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427 |
#8: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5 |
#11: Protein | Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4 |
#48: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533 |
#49: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435 |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules bidkhalejcng
#3: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P62306 #6: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308 #32: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 #37: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 #40: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 #42: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 |
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-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WB
#4: Protein | Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661 |
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#10: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579 |
+Protein , 23 types, 24 molecules Uqv30Q1LNSrRY7KOyGotmfA8
-RNA chain , 4 types, 4 molecules 62Z5
#9: RNA chain | Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: NR_004394.1 / Source: (natural) Homo sapiens (human) |
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#30: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: NR_002716.3 / Source: (natural) Homo sapiens (human) / References: GenBank: 36516 |
#36: RNA chain | Mass: 103963.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#44: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: accession number: X01691.1 / Source: (natural) Homo sapiens (human) / References: GenBank: 36515 |
-Pre-mRNA-splicing factor ... , 3 types, 3 molecules MIP
#26: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7 |
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#41: Protein | Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NAV1 |
#43: Protein | Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64 |
-Splicing factor 3A subunit ... , 3 types, 3 molecules pF4
#45: Protein | Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459 |
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#46: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428 |
#47: Protein | Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874 |
-Non-polymers , 3 types, 3 molecules
#50: Chemical | ChemComp-GTP / |
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#51: Chemical | ChemComp-MG / |
#52: Chemical | ChemComp-IHP / |
-Details
Has ligand of interest | N |
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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 |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R3.5/1 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Average exposure time: 1 sec. / Electron dose: 2.27 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39336 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |