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Yorodumi- EMDB-39013: Cryo-EM Structure of the human minor pre-B complex (pre-precataly... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39013 | ||||||||||||
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Title | Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U12 snRNP part | ||||||||||||
Map data | Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. | ||||||||||||
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 U11/U12 snRNP / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...U11/U12 snRNP / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / blastocyst formation / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / 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 / U2-type prespliceosome / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / U5 snRNP / U2 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / negative regulation of protein catabolic process / stem cell differentiation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / nuclear matrix / mRNA splicing, via spliceosome / mRNA processing / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / chromatin remodeling / nuclear body / nuclear speck / mRNA binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.66 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_39013.map.gz | 406.9 MB | EMDB map data format | |
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Header (meta data) | emd-39013-v30.xml emd-39013.xml | 34.1 KB 34.1 KB | Display Display | EMDB header |
Images | emd_39013.png | 92.4 KB | ||
Filedesc metadata | emd-39013.cif.gz | 10.3 KB | ||
Others | emd_39013_half_map_1.map.gz emd_39013_half_map_2.map.gz | 408.1 MB 408.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39013 | HTTPS FTP |
-Validation report
Summary document | emd_39013_validation.pdf.gz | 980.3 KB | Display | EMDB validaton report |
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Full document | emd_39013_full_validation.pdf.gz | 979.9 KB | Display | |
Data in XML | emd_39013_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_39013_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39013 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39013 | HTTPS FTP |
-Related structure data
Related structure data | 8y7eMC 8y6oC M: atomic model generated by this map C: citing same article (ref.) |
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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_39013.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. | ||||||||||||||||||||
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: Author Stated:The atomic coordinates of U12 snRNP from...
File | emd_39013_half_map_1.map | ||||||||||||
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Annotation | Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Author Stated:The atomic coordinates of U12 snRNP from...
File | emd_39013_half_map_2.map | ||||||||||||
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Annotation | Author Stated:The atomic coordinates of U12 snRNP from human minor Bact complex (PDB code: 7DVQ) were docked into the low-pass filtered bulky density lobe next to the U4atac/U6atac region. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human minor pre-B complex (U12 snRNP part)
+Supramolecule #1: human minor pre-B complex (U12 snRNP part)
+Macromolecule #1: pre-mRNA
+Macromolecule #9: U12 snRNA
+Macromolecule #2: Splicing factor 3B subunit 1
+Macromolecule #3: Splicing factor 3B subunit 2
+Macromolecule #4: Splicing factor 3B subunit 3
+Macromolecule #5: Splicing factor 3B subunit 4
+Macromolecule #6: Splicing factor 3B subunit 6
+Macromolecule #7: PHD finger-like domain-containing protein 5A
+Macromolecule #8: Splicing factor 3B subunit 5
+Macromolecule #10: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #11: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #12: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #13: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #14: Small nuclear ribonucleoprotein E
+Macromolecule #15: Small nuclear ribonucleoprotein F
+Macromolecule #16: Small nuclear ribonucleoprotein G
+Macromolecule #17: Sodium channel modifier 1
+Macromolecule #18: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.9 |
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: 4.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107724 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |