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Yorodumi- EMDB-6889: cryo-EM structure of a human activated spliceosome (mature Bact) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6889 | ||||||||||||
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Title | cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. | ||||||||||||
Map data | Cryo-EM structure of the human activated spliceosome (mature Bact) at 5.1 angstrom resolution | ||||||||||||
Sample |
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Function / homology | Function and homology information RES complex / maintenance of RNA location / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding ...RES complex / maintenance of RNA location / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / 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 / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / poly(A) binding / U12-type spliceosomal complex / methylosome / miRNA processing / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / pre-mRNA binding / 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 / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / pattern recognition receptor activity / lipid biosynthetic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / protein K63-linked ubiquitination / regulation of RNA splicing / antiviral innate immune response / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / RNA processing / U2 snRNA binding / regulation of DNA repair / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / Cajal body / 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 / lipid droplet Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) / unidentified adenovirus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.1 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_6889.map.gz | 228.5 MB | EMDB map data format | |
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Header (meta data) | emd-6889-v30.xml emd-6889.xml | 79.3 KB 79.3 KB | Display Display | EMDB header |
Images | emd_6889.png | 171.8 KB | ||
Others | emd_6889_additional.map.gz | 59.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6889 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6889 | HTTPS FTP |
-Validation report
Summary document | emd_6889_validation.pdf.gz | 530.4 KB | Display | EMDB validaton report |
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Full document | emd_6889_full_validation.pdf.gz | 529.9 KB | Display | |
Data in XML | emd_6889_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_6889_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6889 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6889 | HTTPS FTP |
-Related structure data
Related structure data | 5z56MC 6890C 6891C 5z57C 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_6889.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 (mature Bact) at 5.1 angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: local map for SF3b region of the human...
File | emd_6889_additional.map | ||||||||||||
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Annotation | local map for SF3b region of the human activated spliceosome at 4.2 angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human activated spliceosome
+Supramolecule #1: human activated 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: 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: RING finger protein 113A
+Macromolecule #35: Protein BUD31 homolog
+Macromolecule #36: Pre-mRNA-splicing factor RBM22
+Macromolecule #37: Spliceosome-associated protein CWC15 homolog
+Macromolecule #38: Skip
+Macromolecule #39: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #40: Pleiotropic regulator 1
+Macromolecule #41: Serine/arginine repetitive matrix protein 2
+Macromolecule #42: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #43: Pre-mRNA-processing factor 17
+Macromolecule #44: Smad nuclear-interacting protein 1
+Macromolecule #45: RNA-binding motif protein, X-linked 2
+Macromolecule #46: BUD13 homolog
+Macromolecule #47: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
+Macromolecule #48: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
+Macromolecule #49: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #2: U5 snRNA
+Macromolecule #13: U6 snRNA
+Macromolecule #14: pre-mRNA
+Macromolecule #15: U2 snRNA
+Macromolecule #50: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #51: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: 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, 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 |