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Yorodumi- PDB-5z56: cryo-EM structure of a human activated spliceosome (mature Bact) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z56 | ||||||||||||
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Title | cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. | ||||||||||||
Components |
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Keywords | SPLICING / human activated spliceosome / mature Bact / pre-mRNA splicing | ||||||||||||
Function / homology | Function and homology information 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 / 3'-5' RNA helicase activity / U2 snRNP binding ...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 / 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 / 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 / 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 / U2-type precatalytic spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / pattern recognition receptor activity / lipid biosynthetic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / 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 / U5 snRNA binding / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / RNA processing / U2 snRNA binding / regulation of DNA repair / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / Cajal body / negative regulation of canonical NF-kappaB signal transduction / 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 / lipid droplet Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) unidentified adenovirus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Zhang, X. / Yan, C. / Zhan, X. / Li, L. / Lei, J. / Shi, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell Res / Year: 2018 Title: Structure of the human activated spliceosome in three conformational states. Authors: Xiaofeng Zhang / Chuangye Yan / Xiechao Zhan / Lijia Li / Jianlin Lei / Yigong Shi / Abstract: During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to ...During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B and the B-to-B transitions, which ultimately prime the active site for the branching reaction. | ||||||||||||
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 | 5z56.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5z56.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5z56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z56_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5z56_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 5z56_validation.xml.gz | 433.4 KB | Display | |
Data in CIF | 5z56_validation.cif.gz | 697.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z56 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z56 | HTTPS FTP |
-Related structure data
Related structure data | 6889MC 6890C 6891C 5z57C 5z58C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 18 types, 19 molecules ACbi6JLQMNPRSTUXYZx
+RNA chain , 4 types, 4 molecules BFGH
+U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE
+Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahcjdkfmelgn
+U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op
+Splicing factor 3A subunit ... , 3 types, 3 molecules wuv
+Splicing factor 3B subunit ... , 6 types, 6 molecules 123457
+Pre-mRNA-processing factor ... , 2 types, 5 molecules qrstW
+Pre-mRNA-splicing factor ... , 4 types, 4 molecules KIOV
+Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules zy
+Non-polymers , 4 types, 21 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 activated spliceosome / Type: COMPLEX / Entity ID: #1-#49 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.9 / Details: 20 mM HEPES-KOH, 150 mM NaCl, 1.5 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27405 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Highest resolution: 5.1 Å |