[English] 日本語
Yorodumi- EMDB-6890: Cryo-EM structure of the human activated spliceosome (late Bact) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6890 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||
Map data | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||
Sample |
| ||||||||||||
Function / homology | Function and homology information RES complex / U11/U12 snRNP / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 3'-5' RNA helicase activity / B-WICH complex ...RES complex / U11/U12 snRNP / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 3'-5' RNA helicase activity / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / 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) / splicing factor binding / embryonic brain development / methylosome / protein methylation / U12-type spliceosomal complex / miRNA processing / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / poly(A) binding / positive regulation of androgen receptor activity / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / : / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2 snRNP / SAGA complex / positive regulation of transcription by RNA polymerase III / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / pattern recognition receptor activity / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / WD40-repeat domain binding / precatalytic spliceosome / cyclosporin A binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / protein K63-linked ubiquitination / antiviral innate immune response / mRNA 3'-splice site recognition / blastocyst development / 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 / U5 snRNP / regulation of DNA repair / positive regulation of viral genome replication / Cajal body / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / RNA processing / canonical NF-kappaB signal transduction / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / U1 snRNA binding / translation elongation factor activity / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / lipid droplet / positive regulation of RNA splicing / RNA splicing / response to cocaine / nuclear receptor coactivator activity Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) / unidentified adenovirus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||||||||
Authors | Zhang X / Yan C / Zhan X / Li L / Lei J / Shi Y | ||||||||||||
Funding support | China, 3 items
| ||||||||||||
Citation | Journal: Cell Res / Year: 2018 Title: Structure of the human activated spliceosome in three conformational states. Authors: Xiaofeng Zhang / Chuangye Yan / Xiechao Zhan / Lijia Li / Jianlin Lei / Yigong Shi / Abstract: During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to ...During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B and the B-to-B transitions, which ultimately prime the active site for the branching reaction. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6890.map.gz | 228.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6890-v30.xml emd-6890.xml | 75.2 KB 75.2 KB | Display Display | EMDB header |
Images | emd_6890.png | 171.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6890 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6890 | HTTPS FTP |
-Related structure data
Related structure data | 5z57MC 6889C 6891C 5z56C 5z58C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6890.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : late Bact splieosome
+Supramolecule #1: late Bact splieosome
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #6: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #7: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #8: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #9: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #10: Small nuclear ribonucleoprotein F
+Macromolecule #11: Small nuclear ribonucleoprotein E
+Macromolecule #12: Small nuclear ribonucleoprotein G
+Macromolecule #16: U2 small nuclear ribonucleoprotein A'
+Macromolecule #17: U2 small nuclear ribonucleoprotein B''
+Macromolecule #18: Splicing factor 3A subunit 3
+Macromolecule #19: Splicing factor 3A subunit 1
+Macromolecule #20: Splicing factor 3A subunit 2
+Macromolecule #21: Splicing factor 3B subunit 1
+Macromolecule #22: Splicing factor 3B subunit 2
+Macromolecule #23: Splicing factor 3B subunit 3
+Macromolecule #24: Splicing factor 3B subunit 4
+Macromolecule #25: Splicing factor 3B subunit 6
+Macromolecule #26: PHD finger-like domain-containing protein 5A
+Macromolecule #27: Splicing factor 3B subunit 5
+Macromolecule #28: Crooked neck-like protein 1
+Macromolecule #29: Cell division cycle 5-like protein
+Macromolecule #30: Pre-mRNA-processing factor 19
+Macromolecule #31: Pre-mRNA-splicing factor SPF27
+Macromolecule #32: Pre-mRNA-splicing factor SYF1
+Macromolecule #33: Intron-binding protein aquarius
+Macromolecule #34: Protein BUD31 homolog
+Macromolecule #35: Pre-mRNA-splicing factor RBM22
+Macromolecule #36: Spliceosome-associated protein CWC15 homolog
+Macromolecule #37: Skip
+Macromolecule #38: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #39: Pleiotropic regulator 1
+Macromolecule #40: Serine/arginine repetitive matrix protein 2
+Macromolecule #41: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #42: Pre-mRNA-processing factor 17
+Macromolecule #43: Smad nuclear-interacting protein 1
+Macromolecule #44: RNA-binding motif protein, X-linked 2
+Macromolecule #45: BUD13 homolog
+Macromolecule #46: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+Macromolecule #47: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #2: U5 snRNA
+Macromolecule #13: U6 snRNA
+Macromolecule #14: pre-mRNA
+Macromolecule #15: U2 snRNA
+Macromolecule #48: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #49: ALANINE
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 / Details: 20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
---|---|
Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final 3D classification | Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 14316 |