+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4255 | |||||||||
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Title | human Bact spliceosome core structure | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / B-WICH complex / regulation of vitamin D receptor signaling pathway / splicing factor binding / embryonic brain development ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / B-WICH complex / regulation of vitamin D receptor signaling pathway / splicing factor binding / embryonic brain development / U12-type spliceosomal complex / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / Prp19 complex / blastocyst formation / positive regulation of androgen receptor activity / mRNA 3'-end processing / : / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / SAGA complex / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / regulation of RNA splicing / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNP / retinoic acid receptor signaling pathway / localization / regulation of DNA repair / Cajal body / U2 snRNA binding / U6 snRNA binding / RHOBTB2 GTPase cycle / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / U1 snRNA binding / cellular response to retinoic acid / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / RNA splicing / positive regulation of protein export from nucleus / response to cocaine / nuclear receptor coactivator activity / DNA damage checkpoint signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / stem cell differentiation / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / positive regulation of neuron projection development / NOTCH1 Intracellular Domain Regulates Transcription / mRNA splicing, via spliceosome / fibrillar center / mRNA processing / Constitutive Signaling by NOTCH1 PEST Domain Mutants Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Haselbach D / Komarov I / Agafonov D / Hartmuth K / Graf B / Kastner B / Luehrmann R / Stark H | |||||||||
Citation | Journal: Cell / Year: 2018 Title: Structure and Conformational Dynamics of the Human Spliceosomal B Complex. Authors: David Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark / Abstract: The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation. | |||||||||
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_4255.map.gz | 25.1 MB | EMDB map data format | |
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Header (meta data) | emd-4255-v30.xml emd-4255.xml | 54.1 KB 54.1 KB | Display Display | EMDB header |
Images | emd_4255.png | 53.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4255 | HTTPS FTP |
-Related structure data
Related structure data | 6ff4MC 4233C 4234C 4235C 4236C 4237C 4238C 4239C 4240C 4247C 4248C 4249C 4250C 4251C 4252C 4253C 4254C 6ff7C C: citing same article (ref.) M: atomic model generated by this map |
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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_4255.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : human Bact spliceosome state 1 unmasked
+Supramolecule #1: human Bact spliceosome state 1 unmasked
+Macromolecule #1: RNA-binding motif protein, X-linked 2
+Macromolecule #3: BUD13 homolog
+Macromolecule #6: Splicing factor 3A subunit 2
+Macromolecule #7: Splicing factor 3B subunit 2
+Macromolecule #8: Pre-mRNA-processing-splicing factor 8
+Macromolecule #9: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #10: SNW domain-containing protein 1
+Macromolecule #11: Pleiotropic regulator 1
+Macromolecule #12: Pre-mRNA-processing factor 17
+Macromolecule #13: Cell division cycle 5-like protein
+Macromolecule #14: Crooked neck-like protein 1
+Macromolecule #15: Pre-mRNA-splicing factor RBM22
+Macromolecule #16: Protein BUD31 homolog
+Macromolecule #17: Spliceosome-associated protein CWC15 homolog
+Macromolecule #18: Serine/arginine repetitive matrix protein 2
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: Serine/arginine repetitive matrix protein 1
+Macromolecule #22: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
+Macromolecule #23: RING finger protein 113A
+Macromolecule #24: Splicing factor 3B subunit 1
+Macromolecule #25: Splicing factor 3B subunit 3
+Macromolecule #26: Splicing factor 3B subunit 5
+Macromolecule #27: PHD finger-like domain-containing protein 5A
+Macromolecule #28: Splicing factor 3B subunit 6
+Macromolecule #2: U2 snRNA
+Macromolecule #4: U5 snRNA
+Macromolecule #5: U6 snRNA
+Macromolecule #21: pre mRNA
+Macromolecule #29: MAGNESIUM ION
+Macromolecule #30: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #31: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #32: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: blot with blotting sensor. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Specialist optics | Spherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Alignment procedure | Coma free - Residual tilt: 14.0 mrad |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 32000 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 308000 |
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CTF correction | Software - Name: Gctf |
Initial angle assignment | Type: OTHER / Software - Name: EMAN2 |
Final 3D classification | Number classes: 220 / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17000 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6ff4: |