+Open data
-Basic information
Entry | Database: PDB / ID: 7b0y | |||||||||||||||
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Title | Structure of a transcribing RNA polymerase II-U1 snRNP complex | |||||||||||||||
Components |
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Keywords | SPLICING / Transcription / co-transcriptional spliceosome assembly | |||||||||||||||
Function / homology | Function and homology information negative regulation of protein refolding / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 7-methylguanosine cap hypermethylation / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...negative regulation of protein refolding / regulation of ATP-dependent activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 7-methylguanosine cap hypermethylation / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / U2-type prespliceosome assembly / methylosome / protein methylation / U12-type spliceosomal complex / pICln-Sm protein complex / U1 snRNP binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / U4 snRNP / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / negative regulation of chaperone-mediated autophagy / : / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / precatalytic spliceosome / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / mRNA Splicing - Minor Pathway / regulation of RNA splicing / RNA polymerase II activity / organelle membrane / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / U5 snRNP / transcription by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / spliceosomal complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / DNA-directed RNA polymerase complex / RNA splicing / mRNA splicing, via spliceosome / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / chromosome / snRNP Assembly Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa domesticus (domestic pig) Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Zhang, S. / Aibara, S. / Vos, S.M. / Agafonov, D.E. / Luehrmann, R. / Cramer, P. | |||||||||||||||
Funding support | 4items
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Citation | Journal: Science / Year: 2021 Title: Structure of a transcribing RNA polymerase II-U1 snRNP complex. Authors: Suyang Zhang / Shintaro Aibara / Seychelle M Vos / Dmitry E Agafonov / Reinhard Lührmann / Patrick Cramer / Abstract: To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA). Here, we report ...To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA). Here, we report the cryo-electron microscopy structure of a mammalian transcribing Pol II-U1 snRNP complex. The structure reveals that Pol II and U1 snRNP interact directly. This interaction positions the pre-mRNA 5' splice site near the RNA exit site of Pol II. Extension of pre-mRNA retains the 5' splice site, leading to the formation of a "growing intron loop." Loop formation may facilitate scanning of nascent pre-mRNA for the 3' splice site, functional pairing of distant intron ends, and prespliceosome assembly. Our results provide a starting point for a mechanistic analysis of cotranscriptional spliceosome assembly and the biogenesis of mRNA isoforms by alternative splicing. | |||||||||||||||
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 | 7b0y.cif.gz | 998.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0y.ent.gz | 802.1 KB | Display | PDB format |
PDBx/mmJSON format | 7b0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0y ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0y | HTTPS FTP |
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-Related structure data
Related structure data | 11972MC 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
-DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ACDEFGIK
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P11414, DNA-directed RNA polymerase |
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#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LCH3 |
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A287ADR4 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LSI7 |
#6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: F1SKN8 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LJZ9 |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P60899 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: F1RKE4 |
-Protein , 3 types, 3 molecules BLj
#2: Protein | Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase |
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#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LN51 |
#24: Protein | Mass: 23686.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q66K91 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LCB2 |
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#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1VYD0 |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 14932.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 14672.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 2 types, 2 molecules Pa
#14: RNA chain | Mass: 46784.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#16: RNA chain | Mass: 52697.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-U1 small nuclear ribonucleoprotein ... , 2 types, 2 molecules bc
#17: Protein | Mass: 51683.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08621 |
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#18: Protein | Mass: 31319.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09012 |
-Small nuclear ribonucleoprotein ... , 6 types, 6 molecules efghik
#19: Protein | Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316 |
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#20: Protein | Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306 |
#21: Protein | Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304 |
#22: Protein | Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308 |
#23: Protein | Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318 |
#25: Protein | Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314 |
-Non-polymers , 2 types, 9 molecules
#26: Chemical | ChemComp-ZN / #27: Chemical | ChemComp-MG / | |
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-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
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Source (natural) |
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Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELDBright-field microscopy |
Image recording | Electron dose: 1.01 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61596 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building |
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