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Yorodumi- EMDB-30637: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-30637 | |||||||||
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Title | Cryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom | |||||||||
Map data | overall EM map of the yeast activated spliceosome (Bact complex) at the average resolution of 2.5 angstrom | |||||||||
Sample |
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Keywords | RNA splicing / spliceosome / Bact complex / Prp2 / Spp2 / ATPase/helicase / activation / SPLICING | |||||||||
Function / homology | Function and homology information maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex ...maintenance of RNA location / RES complex / protein serine/threonine phosphatase inhibitor activity / snoRNA splicing / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / miRNA processing / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / ATPase activator activity / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / mRNA export from nucleus / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nucleic acid binding / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / nuclear speck / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Bai R / Wan R | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2021 Title: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Qi Jia / Jianlin Lei / Yigong Shi / Abstract: Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the ...Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu from the N half and Arg from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing. | |||||||||
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_30637.map.gz | 226.3 MB | EMDB map data format | |
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Header (meta data) | emd-30637-v30.xml emd-30637.xml | 73.6 KB 73.6 KB | Display Display | EMDB header |
Images | emd_30637.png | 103 KB | ||
Filedesc metadata | emd-30637.cif.gz | 20.4 KB | ||
Others | emd_30637_additional_1.map.gz | 221.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30637 | HTTPS FTP |
-Validation report
Summary document | emd_30637_validation.pdf.gz | 613.5 KB | Display | EMDB validaton report |
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Full document | emd_30637_full_validation.pdf.gz | 613 KB | Display | |
Data in XML | emd_30637_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_30637_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30637 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30637 | HTTPS FTP |
-Related structure data
Related structure data | 7dcoMC 7dcpC 7dcqC 7dcrC 7dd3C 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_30637.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | overall EM map of the yeast activated spliceosome (Bact complex) at the average resolution of 2.5 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: EM map of Prp2 region in the Bact complex
File | emd_30637_additional_1.map | ||||||||||||
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Annotation | EM map of Prp2 region in the Bact complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : the activated spliceosome Bact complex
+Supramolecule #1: the activated spliceosome Bact complex
+Macromolecule #1: PRP8 isoform 1
+Macromolecule #3: SNU114 isoform 1
+Macromolecule #4: BRR2 isoform 1
+Macromolecule #5: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #6: BJ4_G0014900.mRNA.1.CDS.1
+Macromolecule #7: SMD1 isoform 1
+Macromolecule #8: BJ4_G0037700.mRNA.1.CDS.1
+Macromolecule #9: Small nuclear ribonucleoprotein E
+Macromolecule #10: Sm protein F
+Macromolecule #11: Small nuclear ribonucleoprotein G
+Macromolecule #15: HLJ1_G0053790.mRNA.1.CDS.1
+Macromolecule #16: BJ4_G0027490.mRNA.1.CDS.1
+Macromolecule #17: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #18: PRP9 isoform 1
+Macromolecule #19: Pre-mRNA-splicing factor PRP21
+Macromolecule #20: PRP11 isoform 1
+Macromolecule #21: HSH155 isoform 1
+Macromolecule #22: HLJ1_G0043010.mRNA.1.CDS.1
+Macromolecule #23: RSE1 isoform 1
+Macromolecule #24: HSH49 isoform 1
+Macromolecule #25: BJ4_G0056610.mRNA.1.CDS.1
+Macromolecule #26: RDS3 complex subunit 10
+Macromolecule #27: Pre-mRNA-splicing factor CEF1
+Macromolecule #28: Pre-mRNA-processing factor 19
+Macromolecule #29: SNT309 isoform 1
+Macromolecule #30: BUD31 isoform 1
+Macromolecule #31: HLJ1_G0054350.mRNA.1.CDS.1
+Macromolecule #32: Pre-mRNA-processing protein 45
+Macromolecule #33: Pre-mRNA-splicing factor SLT11
+Macromolecule #34: Pre-mRNA-splicing factor CWC2
+Macromolecule #35: Pre-mRNA-splicing factor CWC15
+Macromolecule #36: Pre-mRNA leakage protein 1
+Macromolecule #37: SX2_G0027210.mRNA.1.CDS.1
+Macromolecule #38: Pre-mRNA-splicing factor CWC26
+Macromolecule #39: CDC40 isoform 1
+Macromolecule #40: Pre-mRNA-splicing factor CWC21
+Macromolecule #41: CWC22 isoform 1
+Macromolecule #42: Pre-mRNA-splicing factor CWC24
+Macromolecule #43: CWC27 isoform 1
+Macromolecule #44: Pre-mRNA-splicing factor SPP2
+Macromolecule #45: CLF1 isoform 1
+Macromolecule #46: SYF1 isoform 1
+Macromolecule #47: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
+Macromolecule #2: U5 snRNA
+Macromolecule #12: U6 snRNA
+Macromolecule #13: pre-mRNA
+Macromolecule #14: U2 snRNA
+Macromolecule #48: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #49: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #50: MAGNESIUM ION
+Macromolecule #51: CALCIUM ION
+Macromolecule #52: ZINC ION
+Macromolecule #53: water
-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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Grid | Model: Quantifoil / Material: GOLD / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GRAPHENE / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #2 - Film type ID: 3 / Support film - #2 - topology: HOLEY |
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: 50.0 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: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 705371 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |