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Yorodumi- EMDB-6891: Cryo-EM structure of a human activated spliceosome (early Bact) a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6891 | ||||||||||||
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Title | Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom. | ||||||||||||
Map data | Cryo-EM structure of the human activated spliceosome (early Bact) at 4.8 angstrom | ||||||||||||
Sample |
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Function / homology | Function and homology information RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / miRNA processing / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 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 / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / antiviral innate immune response / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / Cajal body / pre-mRNA intronic binding / cellular response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / 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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) / unidentified adenovirus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 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_6891.map.gz | 226.9 MB | EMDB map data format | |
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Header (meta data) | emd-6891-v30.xml emd-6891.xml | 62.1 KB 62.1 KB | Display Display | EMDB header |
Images | emd_6891.png | 163.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6891 | HTTPS FTP |
-Validation report
Summary document | emd_6891_validation.pdf.gz | 489 KB | Display | EMDB validaton report |
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Full document | emd_6891_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | emd_6891_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_6891_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6891 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6891 | HTTPS FTP |
-Related structure data
Related structure data | 5z58MC 6889C 6890C 5z56C 5z57C 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_6891.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 (early Bact) at 4.8 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
+Entire : early Bact spliceosome
+Supramolecule #1: early Bact spliceosome
+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: RING finger protein 113A
+Macromolecule #31: Spliceosome-associated protein CWC15 homolog
+Macromolecule #32: Skip
+Macromolecule #33: Pleiotropic regulator 1
+Macromolecule #34: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #35: Smad nuclear-interacting protein 1
+Macromolecule #36: RNA-binding motif protein, X-linked 2
+Macromolecule #37: BUD13 homolog
+Macromolecule #38: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
+Macromolecule #39: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+Macromolecule #2: U5 snRNA
+Macromolecule #13: U6 snRNA
+Macromolecule #14: pre-mRNA
+Macromolecule #15: U2 snRNA
+Macromolecule #40: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #41: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #42: MAGNESIUM ION
+Macromolecule #43: 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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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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |