[English] 日本語
Yorodumi- EMDB-18225: cryo-EM structure of the human spliceosomal B complex protomer (t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18225 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | spliceosome / pre-catalytic spliceosome / spliceosomal B complex / SPLICING | |||||||||
Function / homology | Function and homology information microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding ...microfibril / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / dense fibrillar component / transcription elongation factor activity / U4/U6 snRNP / positive regulation of androgen receptor activity / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / proline-rich region binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / ubiquitin-like protein conjugating enzyme binding / U4 snRNP / RNA polymerase binding / box C/D snoRNP assembly / U2 snRNP / rRNA modification in the nucleus and cytosol / positive regulation of protein targeting to mitochondrion / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of miRNA metabolic process / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / regulation of alternative mRNA splicing, via spliceosome / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / RNA processing / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / ribonucleoprotein complex binding / pre-mRNA intronic binding / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor coactivator activity / response to cocaine / maturation of LSU-rRNA / maturation of SSU-rRNA / nuclear receptor binding / positive regulation of transcription elongation by RNA polymerase II / small-subunit processome / transcription coregulator activity / spliceosomal complex / protein modification process / mRNA processing / mRNA splicing, via spliceosome / protein tag activity / transcription corepressor activity / cellular response to xenobiotic stimulus / protein-macromolecule adaptor activity / cellular response to tumor necrosis factor / ribosomal small subunit biogenesis / ATPase binding / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / cytosolic large ribosomal subunit / transcription coactivator activity / nuclear speck / cell cycle / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / chromatin / nucleolus / GTP binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
| |||||||||
Citation | Journal: To Be Published Title: New insights into the functions of B complex proteins revealed by cryo-EM of dimerized spliceosomes Authors: Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_18225.map.gz | 493.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-18225-v30.xml emd-18225.xml | 39.8 KB 39.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18225_fsc.xml | 18.3 KB | Display | FSC data file |
Images | emd_18225.png | 40.6 KB | ||
Filedesc metadata | emd-18225.cif.gz | 13.1 KB | ||
Others | emd_18225_half_map_1.map.gz emd_18225_half_map_2.map.gz | 428.4 MB 428.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18225 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18225 | HTTPS FTP |
-Validation report
Summary document | emd_18225_validation.pdf.gz | 882.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_18225_full_validation.pdf.gz | 882 KB | Display | |
Data in XML | emd_18225_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | emd_18225_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18225 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18225 | HTTPS FTP |
-Related structure data
Related structure data | 8q7nMC 8qo9C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_18225.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_18225_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_18225_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : human pre-catalytic spliceosome
+Supramolecule #1: human pre-catalytic spliceosome
+Macromolecule #1: U5 snRNA
+Macromolecule #2: U6 snRNA
+Macromolecule #11: MINX pre-mRNA
+Macromolecule #20: U4 snRNA
+Macromolecule #3: Splicing factor 3A subunit 1
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: Thioredoxin-like protein 4A
+Macromolecule #6: Pre-mRNA-splicing factor 38A
+Macromolecule #7: Microfibrillar-associated protein 1
+Macromolecule #8: NHP2-like protein 1, N-terminally processed
+Macromolecule #9: Protein BUD31 homolog
+Macromolecule #10: WW domain-binding protein 4
+Macromolecule #12: Zinc finger matrin-type protein 2
+Macromolecule #13: Ubiquitin-like protein 5
+Macromolecule #14: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #15: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #16: Pre-mRNA-processing factor 6
+Macromolecule #17: Pre-mRNA-processing-splicing factor 8
+Macromolecule #18: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #19: Transcription elongation regulator 1
+Macromolecule #21: U4/U6 small nuclear ribonucleoprotein Prp3
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |