[English] 日本語
![](img/lk-miru.gif)
- EMDB-3766: Cryo-EM structure of a pre-catalytic human spliceosome primed for... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3766 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) | ||||||||||||
![]() | sharpened, refined map | ||||||||||||
![]() |
| ||||||||||||
Function / homology | ![]() microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding ...microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / 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 / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / protein localization to kinetochore / P-body assembly / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / proline-rich region binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / U3 snoRNA binding / positive regulation of transcription by RNA polymerase III / U1 snRNP / tRNA processing / U2-type prespliceosome / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / mitotic spindle assembly checkpoint signaling / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / protein peptidyl-prolyl isomerization / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / positive regulation of viral genome replication / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||
![]() | Bertram K | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Authors: Karl Bertram / Dmitry E Agafonov / Olexandr Dybkov / David Haselbach / Majety N Leelaram / Cindy L Will / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark / ![]() Abstract: Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B ...Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4/U6 substrate and is poised for the subsequent spliceosome activation step. The molecular organization of several B-specific proteins suggests that they are involved in negatively regulating Brr2, positioning the U6/5'ss helix, and stabilizing the B complex structure. Our results indicate significant differences between the early activation phase of human and yeast spliceosomes. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 285.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 65.5 KB 65.5 KB | Display Display | ![]() |
Images | ![]() | 27.6 KB | ||
Others | ![]() ![]() ![]() | 244.3 MB 246 MB 245.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o9zMC ![]() 3767C ![]() 3768C ![]() 3769C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened, refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: None
File | emd_3766_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: None
File | emd_3766_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: None
File | emd_3766_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : Human B Complex Spliceosome, sharpened map, masked refinement
+Supramolecule #1: Human B Complex Spliceosome, sharpened map, masked refinement
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #2: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #3: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #4: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #5: U4/U6 small nuclear ribonucleoprotein Prp3
+Macromolecule #6: U4/U6 small nuclear ribonucleoprotein Prp4
+Macromolecule #7: Pre-mRNA-processing factor 6
+Macromolecule #8: U4/U6 small nuclear ribonucleoprotein Prp31
+Macromolecule #9: Pre-mRNA-splicing factor 38A
+Macromolecule #10: Thioredoxin-like protein 4A
+Macromolecule #11: Microfibrillar-associated protein 1
+Macromolecule #12: WD40 repeat-containing protein SMU1
+Macromolecule #13: Peptidyl-prolyl cis-trans isomerase H
+Macromolecule #14: Zinc finger matrin-type protein 2
+Macromolecule #15: NHP2-like protein 1
+Macromolecule #16: U4/U6.U5 tri-snRNP-associated protein 1
+Macromolecule #17: WW domain-binding protein 4
+Macromolecule #18: Protein Red
+Macromolecule #19: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #20: Small nuclear ribonucleoprotein F
+Macromolecule #21: Small nuclear ribonucleoprotein E
+Macromolecule #22: Small nuclear ribonucleoprotein G
+Macromolecule #23: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #24: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #25: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #26: U6 snRNA-associated Sm-like protein LSm2
+Macromolecule #27: U6 snRNA-associated Sm-like protein LSm3
+Macromolecule #28: U6 snRNA-associated Sm-like protein LSm4
+Macromolecule #29: U6 snRNA-associated Sm-like protein LSm5
+Macromolecule #30: U6 snRNA-associated Sm-like protein LSm6
+Macromolecule #31: U6 snRNA-associated Sm-like protein LSm7
+Macromolecule #32: U6 snRNA-associated Sm-like protein LSm8
+Macromolecule #33: Splicing factor 3B subunit 1
+Macromolecule #34: Splicing factor 3B subunit 3 (SF3B3)
+Macromolecule #35: Splicing factor 3B subunit 5
+Macromolecule #36: PHD finger-like domain-containing protein 5A
+Macromolecule #37: U2 small nuclear ribonucleoprotein A'
+Macromolecule #38: U2 small nuclear ribonucleoprotein B''
+Macromolecule #39: MINX pre-mRNA
+Macromolecule #40: Human gene for small nuclear RNA U2 (snRNA U2)
+Macromolecule #41: Homo sapiens U4A snRNA
+Macromolecule #42: Homo sapiens U5 A small nuclear RNA
+Macromolecule #43: Homo sapiens RNA, U6 small nuclear 1 (RNU6-1), small nuclear RNA
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-17 / Average exposure time: 0.05 sec. / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
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 | Space: REAL |
---|---|
Output model | ![]() PDB-5o9z: |