+Open data
-Basic information
Entry | Database: PDB / ID: 6ff7 | ||||||
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Title | human Bact spliceosome core structure | ||||||
Components |
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Keywords | SPLICING / spliceosome / human / HELA / BACT / dynamics | ||||||
Function / homology | Function and homology information post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding ...post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / B-WICH complex / generation of catalytic spliceosome for first transesterification step / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / splicing factor binding / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / blastocyst formation / poly(A) binding / positive regulation of androgen receptor activity / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / transcription regulator inhibitor activity / U2 snRNP / nuclear vitamin D receptor binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / positive regulation of transcription by RNA polymerase III / U1 snRNP / RHOBTB1 GTPase cycle / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / pattern recognition receptor activity / lipid biosynthetic process / 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 / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of RNA splicing / SMAD binding / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / antiviral innate immune response / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ff7.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ff7.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 6ff7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 | HTTPS FTP |
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-Related structure data
Related structure data | 4240MC 4233C 4234C 4235C 4236C 4237C 4238C 4239C 4247C 4248C 4249C 4250C 4251C 4252C 4253C 4254C 4255C 6ff4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10160 (Title: Conformational Dynamics of human Bact spliceosome / Data size: 2.8 TB Data #1: aligned and summed micrograph stack of human Bact spliceosome [micrographs - single frame] Data #2: aligned, dose-weighted and summed micrograph stack of human Bact spliceosome [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 17 types, 18 molecules 13ABCDLOQRVty0Ufmq
+RNA chain , 4 types, 4 molecules 256Z
+Splicing factor 3A subunit ... , 3 types, 3 molecules 79p
+Splicing factor 3B subunit ... , 5 types, 6 molecules 8uvxzN
+Pre-mRNA-processing factor ... , 2 types, 5 molecules EGHIJ
+Pre-mRNA-splicing factor ... , 5 types, 5 molecules PKMTw
+Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules SY
+Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules so
+U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules Fr
+U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WX
+Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahbicjdkelgn
+Non-polymers , 5 types, 20 molecules
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human Bact spliceosome / Type: COMPLEX / Entity ID: #1-#50 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 |
EM embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165853 / Symmetry type: POINT |