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Yorodumi- EMDB-11972: Overall map of a transcribing RNA polymerase II-U1 snRNP complex ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11972 | |||||||||||||||
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Title | Overall map of a transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA | |||||||||||||||
Map data | Sharpened map | |||||||||||||||
Sample |
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Keywords | Transcription / Splicing / 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 / 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 / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / 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 / protein methylation / 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 / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / negative regulation of chaperone-mediated autophagy / 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 / positive regulation of mRNA splicing, via spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / organelle membrane / precatalytic spliceosome / RNA polymerase III activity / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / regulation of RNA splicing / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / U5 snRNP / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / spliceosomal snRNP assembly / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / translation initiation factor binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / spliceosomal complex / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / mRNA splicing, via spliceosome / DNA-directed RNA polymerase / chromosome / single-stranded DNA binding / snRNP Assembly Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa domesticus (domestic pig) / synthetic construct (others) / Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Zhang S / Aibara S | |||||||||||||||
Funding support | 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11972.map.gz | 226.7 MB | EMDB map data format | |
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Header (meta data) | emd-11972-v30.xml emd-11972.xml | 50.3 KB 50.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11972_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_11972.png | 76.9 KB | ||
Masks | emd_11972_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-11972.cif.gz | 11.3 KB | ||
Others | emd_11972_additional_1.map.gz emd_11972_half_map_1.map.gz emd_11972_half_map_2.map.gz | 193.7 MB 194 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11972 | HTTPS FTP |
-Validation report
Summary document | emd_11972_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_11972_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_11972_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_11972_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11972 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11972 | HTTPS FTP |
-Related structure data
Related structure data | 7b0yMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11972.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11972_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_11972_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_11972_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_11972_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
+Supramolecule #1: The transcribing RNA polymerase II-U1 snRNP complex with 145-nt RNA
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: Nucleic acids
+Supramolecule #4: U1 snRNP
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: RPB12
+Macromolecule #17: U1 small nuclear ribonucleoprotein 70 kDa
+Macromolecule #18: U1 small nuclear ribonucleoprotein A
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #20: Small nuclear ribonucleoprotein F
+Macromolecule #21: Small nuclear ribonucleoprotein E
+Macromolecule #22: Small nuclear ribonucleoprotein G
+Macromolecule #23: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #24: Small nuclear ribonucleoprotein-associated protein
+Macromolecule #25: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #13: Non-template DNA
+Macromolecule #15: Template DNA
+Macromolecule #14: 145-nt RNA
+Macromolecule #16: U1 snRNA
+Macromolecule #26: ZINC ION
+Macromolecule #27: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R2/2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 100 sec. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.01 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Output model | PDB-7b0y: |