+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 / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...post-spliceosomal complex / 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 / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / miRNA processing / splicing factor binding / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / embryonic brain development / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / Prp19 complex / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / snRNP binding / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation by host of viral transcription / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / transcription regulator inhibitor activity / commitment complex / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / Notch binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / positive regulation of neurogenesis / pattern recognition receptor activity / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / lipid biosynthetic process / U2-type prespliceosome / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / SMAD binding / regulation of RNA splicing / protein K63-linked ubiquitination / protein peptidyl-prolyl isomerization / mRNA 3'-splice site recognition / 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 / U5 snRNA binding 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
Summary document | 6ff7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6ff7_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ff7_validation.xml.gz | 301.2 KB | Display | |
Data in CIF | 6ff7_validation.cif.gz | 543.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 | HTTPS FTP |
-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 FIELD |
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 |