+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 / maintenance of RNA location / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway ...post-spliceosomal complex / RES complex / maintenance of RNA location / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / U7 snRNP / 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 / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / poly(A) binding / U12-type spliceosomal complex / methylosome / miRNA processing / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / commitment complex / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / 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 / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / pattern recognition receptor activity / positive regulation of neurogenesis / lipid biosynthetic process / 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 / generation of catalytic spliceosome for second transesterification step / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / SMAD binding / regulation of alternative mRNA splicing, via spliceosome / protein K63-linked ubiquitination / regulation of RNA splicing / antiviral innate immune response / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly 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 |