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Yorodumi- EMDB-6890: Cryo-EM structure of the human activated spliceosome (late Bact) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6890 | ||||||||||||
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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 |
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Function / homology | Function and homology information RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / B-WICH complex ...RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / 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 / miRNA processing / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / Prp19 complex / positive regulation of androgen receptor activity / poly(A) binding / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / pICln-Sm protein complex / blastocyst formation / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / transcription regulator inhibitor activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / 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 / SAGA complex / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / pattern recognition receptor activity / WD40-repeat domain binding / lipid biosynthetic process / Cajal body / U2-type prespliceosome / cyclosporin A binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / protein K63-linked ubiquitination / blastocyst development / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / U2 snRNA binding / RNA processing / U6 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / pre-mRNA intronic binding / negative regulation of canonical NF-kappaB signal transduction / U1 snRNA binding / antiviral innate immune response / 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 / lipid droplet / RNA splicing / positive regulation of RNA splicing / positive regulation of protein export from nucleus / 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
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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 |
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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_6890.map.gz | 228.2 MB | EMDB map data format | |
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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 |
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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_6890.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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 |
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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 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |