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Yorodumi- EMDB-9621: The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spli... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9621 | |||||||||
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Title | The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) | |||||||||
Map data | The 5.7 Angstrom map of the human pre-B complex | |||||||||
Sample |
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Keywords | Spliceosome / SPLICING | |||||||||
Function / homology | Function and homology information Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease ...Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / RNA localization / R-loop processing / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / U6 snRNP / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / B-WICH complex / 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 / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / U1 snRNP binding / blastocyst formation / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / box C/D snoRNP assembly / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / tRNA processing / U1 snRNP / U3 snoRNA binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of miRNA metabolic process / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / mRNA catabolic process / regulation of RNA splicing / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / Cajal body / ribonucleoprotein complex binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / helicase activity / response to cocaine / maturation of LSU-rRNA Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Zhan X / Yan C | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Res / Year: 2018 Title: Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi / Abstract: The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are ...The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome. | |||||||||
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_9621.map.gz | 226 MB | EMDB map data format | |
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Header (meta data) | emd-9621-v30.xml emd-9621.xml | 65.4 KB 65.4 KB | Display Display | EMDB header |
Images | emd_9621.png | 149.4 KB | ||
Filedesc metadata | emd-9621.cif.gz | 19.3 KB | ||
Others | emd_9621_additional.map.gz | 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9621 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9621 | HTTPS FTP |
-Validation report
Summary document | emd_9621_validation.pdf.gz | 504.6 KB | Display | EMDB validaton report |
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Full document | emd_9621_full_validation.pdf.gz | 504.1 KB | Display | |
Data in XML | emd_9621_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_9621_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9621 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9621 | HTTPS FTP |
-Related structure data
Related structure data | 6ah0MC 9624C 6ahdC 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_9621.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The 5.7 Angstrom map of the human pre-B complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: The low resolution map of the U2 snRNP...
File | emd_9621_additional.map | ||||||||||||
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Annotation | The low resolution map of the U2 snRNP part of the human pre-B complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Spliceosome
+Supramolecule #1: Spliceosome
+Macromolecule #1: U5snRNA
+Macromolecule #11: U6snRNA
+Macromolecule #19: pre-mRNA
+Macromolecule #20: U2snRNA
+Macromolecule #40: U4snRNA
+Macromolecule #2: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #3: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #4: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #5: Small nuclear ribonucleoprotein F
+Macromolecule #6: Small nuclear ribonucleoprotein E
+Macromolecule #7: Small nuclear ribonucleoprotein G
+Macromolecule #8: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #9: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #10: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #12: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #13: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #14: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #16: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #17: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #18: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #21: U2 small nuclear ribonucleoprotein A'
+Macromolecule #22: U2 small nuclear ribonucleoprotein B''
+Macromolecule #23: Splicing factor 3A subunit 1
+Macromolecule #24: Splicing factor 3A subunit 2
+Macromolecule #25: Splicing factor 3A subunit 3
+Macromolecule #26: Splicing factor 3B subunit 1
+Macromolecule #27: Splicing factor 3B subunit 2
+Macromolecule #28: Splicing factor 3B subunit 3
+Macromolecule #29: Splicing factor 3B subunit 4
+Macromolecule #30: Splicing factor 3B subunit 6
+Macromolecule #31: PHD finger-like domain-containing protein 5A
+Macromolecule #32: Splicing factor 3B subunit 5
+Macromolecule #33: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #34: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #35: Pre-mRNA-processing factor 6
+Macromolecule #36: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #37: NHP2-like protein 1
+Macromolecule #38: Thioredoxin-like protein 4A
+Macromolecule #39: U4/U6.U5 tri-snRNP-associated protein 2
+Macromolecule #41: Probable ATP-dependent RNA helicase DDX23
+Macromolecule #42: Pre-mRNA-processing-splicing factor 8
+Macromolecule #43: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #44: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #45: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #46: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 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
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186162 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |