+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 / embryonic brain development / splicing factor binding ...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 / embryonic brain development / splicing factor binding / U12-type spliceosomal complex / nuclear retinoic acid receptor binding / Prp19 complex / positive regulation of androgen receptor activity / mRNA 3'-end processing / blastocyst formation / RNA splicing, via transesterification reactions / pre-mRNA binding / U2-type catalytic step 1 spliceosome / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / Cajal body / positive regulation of neurogenesis / U2-type prespliceosome / cyclosporin A binding / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / retinoic acid receptor signaling pathway / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / regulation of RNA splicing / mRNA 3'-splice site recognition / protein peptidyl-prolyl isomerization / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding / U5 snRNP / RHOBTB2 GTPase cycle / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor coactivator activity / DNA damage checkpoint signaling / response to cocaine / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein catabolic process / nuclear receptor binding / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / spliceosomal complex / RING-type E3 ubiquitin transferase / B-WICH complex positively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / fibrillar center / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of neuron projection development / nuclear matrix / mRNA splicing, via spliceosome 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 |
-Validation report
Summary document | emd_4255_validation.pdf.gz | 233.7 KB | Display | EMDB validaton report |
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Full document | emd_4255_full_validation.pdf.gz | 232.8 KB | Display | |
Data in XML | emd_4255_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4255 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Alignment procedure | Coma free - Residual tilt: 14.0 mrad |
Specialist optics | Spherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements |
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 |
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 FIELD / Cs: 0.001 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6ff4: |