+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18529 | |||||||||
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Title | Cryo-EM structure of a human spliceosomal B complex protomer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | spliceosome / SPLICING | |||||||||
Function / homology | Function and homology information DNA topoisomerase binding / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA ...DNA topoisomerase binding / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / snRNP binding / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / protein kinase B binding / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / U6 snRNP / box C/D sno(s)RNA binding / positive regulation of primary miRNA processing / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / alternative mRNA splicing, via spliceosome / 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 / mRNA splice site recognition / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / transcription elongation factor activity / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / protein localization to kinetochore / 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 / spliceosomal tri-snRNP complex / P granule / U4 snRNA binding / telomerase holoenzyme complex / box C/D methylation guide snoRNP 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 / 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 / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / tRNA processing / U1 snRNP / positive regulation of protein targeting to mitochondrion / U3 snoRNA binding / nuclear-transcribed mRNA catabolic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of miRNA metabolic process / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / mitotic spindle assembly checkpoint signaling / spliceosomal complex assembly / oligodendrocyte differentiation / mRNA Splicing - Minor Pathway / negative regulation of transcription elongation by RNA polymerase II / regulation of alternative mRNA splicing, via spliceosome / mRNA catabolic process / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / Processing of Capped Intron-Containing Pre-mRNA / MLL1 complex / spliceosomal tri-snRNP complex assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.29 Å | |||||||||
Authors | Zhang Z / Kumar V / Dybkov O / Will CL / Urlaub H / Stark H / Luehrmann R | |||||||||
Funding support | Germany, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18529.map.gz | 51 MB | EMDB map data format | |
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Header (meta data) | emd-18529-v30.xml emd-18529.xml | 78 KB 78 KB | Display Display | EMDB header |
Images | emd_18529.png | 74.8 KB | ||
Filedesc metadata | emd-18529.cif.gz | 21.5 KB | ||
Others | emd_18529_half_map_1.map.gz emd_18529_half_map_2.map.gz | 51.6 MB 51.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18529 | HTTPS FTP |
-Validation report
Summary document | emd_18529_validation.pdf.gz | 816.5 KB | Display | EMDB validaton report |
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Full document | emd_18529_full_validation.pdf.gz | 816.1 KB | Display | |
Data in XML | emd_18529_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_18529_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18529 | HTTPS FTP |
-Related structure data
Related structure data | 8qo9MC 8q7nC 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_18529.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18529_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18529_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human spliceosomal B complex
+Supramolecule #1: human spliceosomal B complex
+Macromolecule #1: Splicing factor 3B subunit 4
+Macromolecule #2: Splicing factor 3A subunit 2
+Macromolecule #3: Splicing factor 3A subunit 3
+Macromolecule #4: Splicing factor 3B subunit 2
+Macromolecule #5: Splicing factor 3B subunit 5
+Macromolecule #7: Splicing factor 3B subunit 3
+Macromolecule #8: PHD finger-like domain-containing protein 5A
+Macromolecule #9: Splicing factor 3B subunit 1
+Macromolecule #10: Splicing factor 3B subunit 6
+Macromolecule #11: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #12: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #13: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #14: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #15: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #16: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #17: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #18: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #20: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #21: Small nuclear ribonucleoprotein F
+Macromolecule #22: Small nuclear ribonucleoprotein E
+Macromolecule #23: Small nuclear ribonucleoprotein G
+Macromolecule #24: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #25: U2 small nuclear ribonucleoprotein B''
+Macromolecule #26: U2 small nuclear ribonucleoprotein A'
+Macromolecule #27: Splicing factor 3A subunit 1
+Macromolecule #28: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #29: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #30: Protein Red
+Macromolecule #31: WD40 repeat-containing protein SMU1
+Macromolecule #32: Serine/arginine-rich splicing factor 1
+Macromolecule #33: Peptidyl-prolyl cis-trans isomerase H
+Macromolecule #35: Protein BUD31 homolog
+Macromolecule #36: Thioredoxin-like protein 4A
+Macromolecule #37: WW domain-binding protein 4
+Macromolecule #38: Microfibrillar-associated protein 1
+Macromolecule #40: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #41: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #42: Pre-mRNA-processing factor 6
+Macromolecule #43: Pre-mRNA-processing-splicing factor 8
+Macromolecule #44: Pre-mRNA-splicing factor 38A
+Macromolecule #45: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #46: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #47: NHP2-like protein 1, N-terminally processed
+Macromolecule #48: Transcription elongation regulator 1
+Macromolecule #51: Zinc finger matrin-type protein 2
+Macromolecule #52: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #53: Ubiquitin-like protein 5
+Macromolecule #6: U2 snRNA
+Macromolecule #34: U5 snRNA
+Macromolecule #39: MINX pre-mRNA
+Macromolecule #49: U4 snRNA
+Macromolecule #50: U6 snRNA
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 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: 5.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ad initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50321 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |