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Yorodumi- PDB-6id0: Cryo-EM structure of a human intron lariat spliceosome prior to P... -
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-Basic information
Entry | Database: PDB / ID: 6id0 | |||||||||
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Title | Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution | |||||||||
Components |
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Keywords | SPLICING / Human Intron Lariat Spliceosome | |||||||||
Function / homology | Function and homology information snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP / 7-methylguanosine cap hypermethylation / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / histone pre-mRNA 3'end processing complex ...snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / post-mRNA release spliceosomal complex / U7 snRNP / 7-methylguanosine cap hypermethylation / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / histone pre-mRNA 3'end processing complex / generation of catalytic spliceosome for first transesterification step / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of vitamin D receptor signaling pathway / U2-type prespliceosome assembly / methylosome / protein methylation / U12-type spliceosomal complex / embryonic brain development / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / nuclear retinoic acid receptor binding / RNA splicing, via transesterification reactions / Prp19 complex / U4 snRNP / spliceosomal tri-snRNP complex / poly(A) binding / small nuclear ribonucleoprotein complex / P granule / positive regulation of androgen receptor activity / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / U1 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / ubiquitin-ubiquitin ligase activity / spliceosomal complex assembly / U2-type prespliceosome / RUNX3 regulates NOTCH signaling / K63-linked polyubiquitin modification-dependent protein binding / NOTCH4 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / positive regulation of neurogenesis / lipid biosynthetic process / NOTCH3 Intracellular Domain Regulates Transcription / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / mRNA Splicing - Minor Pathway / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / blastocyst development / RNA processing / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / retinoic acid receptor signaling pathway / spliceosomal snRNP assembly / positive regulation of viral genome replication / embryonic organ development / Cajal body / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / protein peptidyl-prolyl isomerization / U1 snRNA binding / gastrulation / cellular response to retinoic acid / translation elongation factor activity / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / lipid droplet Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zhang, X. / Zhan, X. / Yan, C. / Shi, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Res / Year: 2019 Title: Structures of the human spliceosomes before and after release of the ligated exon. Authors: Xiaofeng Zhang / Xiechao Zhan / Chuangye Yan / Wenyu Zhang / Dongliang Liu / Jianlin Lei / Yigong Shi / Abstract: Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ...Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3'-splice site is recognized by the junction between the 5'-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6id0.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6id0.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6id0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6id0 ftp://data.pdbj.org/pub/pdb/validation_reports/id/6id0 | HTTPS FTP |
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-Related structure data
Related structure data | 9646MC 9645C 9647C 6iczC 6id1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 12 types, 13 molecules ACEJLNPRTUbiQ
#1: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9 | ||
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#3: Protein | Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029 | ||
#4: Protein | Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7 | ||
#6: Protein | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0 | ||
#7: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459 | ||
#9: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223 | ||
#11: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013 | ||
#12: Protein | Mass: 61770.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573 | ||
#14: Protein | Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660 | ||
#18: Protein | Mass: 103976.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TBE0 | ||
#21: Protein | Mass: 23686.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q66K91, UniProt: P14678*PLUS #31: Protein | | Mass: 171502.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60306, RNA helicase |
-RNA chain , 4 types, 4 molecules BFGH
#2: RNA chain | Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981 |
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#5: RNA chain | Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#16: RNA chain | Mass: 87186.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#17: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340097 |
-Pre-mRNA-splicing factor ... , 4 types, 4 molecules MOIK
#8: Protein | Mass: 28780.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95926 |
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#10: Protein | Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64 |
#19: Protein | Mass: 100148.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7 |
#28: Protein | Mass: 26163.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75934 |
-Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy
#13: Protein | Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase |
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#32: Protein | Mass: 33475.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase |
-Pre-mRNA-processing factor ... , 2 types, 5 molecules Wqrst
#15: Protein | Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508 |
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#27: Protein | Mass: 55245.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase |
-Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn
#20: Protein | Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 #22: Protein | Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 #23: Protein | Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 #24: Protein | Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306 #25: Protein | Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 #26: Protein | Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308 |
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-U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op
#29: 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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#30: Protein | Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579 |
-Non-polymers , 4 types, 16 molecules
#33: Chemical | ChemComp-IHP / | ||
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#34: Chemical | ChemComp-GTP / | ||
#35: Chemical | ChemComp-MG / #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 |
-Sample preparation
Component | Name: Human Intron Lariat Spliceosome / Type: COMPLEX / Entity ID: #1-#32 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 390072 / Symmetry type: POINT |
Refinement | Highest resolution: 2.9 Å |