+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ff4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | human Bact spliceosome core structure | |||||||||
![]() |
| |||||||||
![]() | SPLICING / spliceosome / human / HELA / BACT / dynamics | |||||||||
Function / homology | ![]() 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 / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / RHOBTB1 GTPase cycle / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / 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 localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / localization / retinoic acid receptor signaling pathway / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / RHOBTB2 GTPase cycle / U2 snRNA binding / regulation of DNA repair / U6 snRNA binding / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / Cajal body / cellular response to retinoic acid / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor coactivator activity / response to cocaine / 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 / NOTCH1 Intracellular Domain Regulates Transcription / mRNA processing / fibrillar center / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Haselbach, D. / Komarov, I. / Agafonov, D. / Hartmuth, K. / Graf, B. / Kastner, B. / Luehrmann, R. / Stark, H. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 206.8 KB | Display | |
Data in CIF | ![]() | 329.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4255MC ![]() 4233C ![]() 4234C ![]() 4235C ![]() 4236C ![]() 4237C ![]() 4238C ![]() 4239C ![]() 4240C ![]() 4247C ![]() 4248C ![]() 4249C ![]() 4250C ![]() 4251C ![]() 4252C ![]() 4253C ![]() 4254C ![]() 6ff7C C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 15 types, 15 molecules 137ABCDELOPQRty
#1: Protein | Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#3: Protein | Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#23: Protein | Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 4 types, 4 molecules 256Z
#2: RNA chain | Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#4: RNA chain | Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: RNA chain | Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: RNA chain | Mass: 153787.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Splicing factor 3B subunit ... , 5 types, 5 molecules 8uvxz
#7: Protein | Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#24: Protein | Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules SY
#18: Protein | Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#20: Protein | Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Vs
#19: Protein | Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#22: Protein | Mass: 53941.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 16 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
#29: Chemical | ChemComp-MG / #30: Chemical | ChemComp-IHP / | #31: Chemical | ChemComp-GTP / | #32: Chemical | ChemComp-ZN / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: human Bact spliceosome state 1 unmasked / Type: COMPLEX / Entity ID: #1-#4, #6-#28 / Source: NATURAL | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 4.5 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 277 K / Details: blot with blotting sensor |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 800 nm / Cs: 0.001 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 14 mradians |
Image recording | Average exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 32000 |
EM imaging optics | Spherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-
Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 308000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17000 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
|