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Yorodumi- EMDB-38993: Cryo-EM Structure of the human minor pre-B complex (pre-precataly... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38993 | ||||||||||||
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Title | Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | spliceosome / minor spliceosome / U11 snRNP / U12 snRNP / U4atac / U6atac / CENATAC / TXNL4B / U11 snRNA / minor tri-snRNP / U12-type intron / SPLICING/RNA / SPLICING-RNA complex | ||||||||||||
Function / homology | Function and homology information negative regulation of centrosome duplication / spliceosomal snRNP complex / ribonucleoprotein complex localization / chromosome separation / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / positive regulation of hippo signaling / RNA localization / R-loop processing ...negative regulation of centrosome duplication / spliceosomal snRNP complex / ribonucleoprotein complex localization / chromosome separation / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / positive regulation of hippo signaling / RNA localization / R-loop processing / U4atac snRNA binding / regulation of mitotic cell cycle spindle assembly checkpoint / box C/D sno(s)RNA binding / snRNA binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 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 / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / 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 / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / U3 snoRNA binding / U1 snRNP / Cajal body / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / intercellular bridge / precatalytic spliceosome / regulation of protein catabolic process / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / response to glucocorticoid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of protein export from nucleus / response to cocaine / helicase activity / maturation of SSU-rRNA / small-subunit processome / spliceosomal complex / kinetochore / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / ATPase binding / ribosomal small subunit biogenesis / protein-macromolecule adaptor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / cellular response to lipopolysaccharide Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | ||||||||||||
Authors | Bai R / Yuan M / Zhang P / Luo T / Shi Y / Wan R | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Science / Year: 2024 Title: Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Authors: Rui Bai / Meng Yuan / Pu Zhang / Ting Luo / Yigong Shi / Ruixue Wan / Abstract: The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we ...The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38993.map.gz | 483.3 MB | EMDB map data format | |
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Header (meta data) | emd-38993-v30.xml emd-38993.xml | 58.1 KB 58.1 KB | Display Display | EMDB header |
Images | emd_38993.png | 85.1 KB | ||
Filedesc metadata | emd-38993.cif.gz | 17.4 KB | ||
Others | emd_38993_half_map_1.map.gz emd_38993_half_map_2.map.gz | 475.3 MB 475.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38993 | HTTPS FTP |
-Validation report
Summary document | emd_38993_validation.pdf.gz | 866.1 KB | Display | EMDB validaton report |
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Full document | emd_38993_full_validation.pdf.gz | 865.6 KB | Display | |
Data in XML | emd_38993_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_38993_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38993 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38993 | HTTPS FTP |
-Related structure data
Related structure data | 8y6oMC 8y7eC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38993.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38993_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38993_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human minor pre-B complex
+Supramolecule #1: human minor pre-B complex
+Macromolecule #1: pre-mRNA
+Macromolecule #2: U5 snRNA
+Macromolecule #17: U4atac snRNA
+Macromolecule #18: U6atac snRNA
+Macromolecule #24: U11 snRNA
+Macromolecule #3: Pre-mRNA-processing-splicing factor 8
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #6: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #7: Pre-mRNA-processing factor 6
+Macromolecule #8: Thioredoxin-like protein 4B
+Macromolecule #9: Probable ATP-dependent RNA helicase DDX23
+Macromolecule #10: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #11: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #14: Small nuclear ribonucleoprotein E
+Macromolecule #15: Small nuclear ribonucleoprotein F
+Macromolecule #16: Small nuclear ribonucleoprotein G
+Macromolecule #19: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #20: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #21: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #22: NHP2-like protein 1
+Macromolecule #23: Centrosomal AT-AC splicing factor
+Macromolecule #25: Zinc finger matrin-type protein 5
+Macromolecule #26: U11/U12 small nuclear ribonucleoprotein 35 kDa protein
+Macromolecule #27: U11/U12 small nuclear ribonucleoprotein 25 kDa protein
+Macromolecule #28: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
+Macromolecule #29: Programmed cell death protein 7
+Macromolecule #30: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #31: U4/U6.U5 tri-snRNP-associated protein 2
+Macromolecule #32: Serine/threonine-protein kinase PRP4 homolog
+Macromolecule #33: MAGNESIUM ION
+Macromolecule #34: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #35: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #36: 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 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 388888 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |