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- PDB-5z57: Cryo-EM structure of the human activated spliceosome (late Bact) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z57 | ||||||||||||
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Title | Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom | ||||||||||||
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![]() | SPLICING / spliceosome / cryo-EM structure / activated spliceosome / late Bact complex / pre-mRNA splicing | ||||||||||||
Function / homology | ![]() RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 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 / histone pre-mRNA 3'end processing complex ...RES complex / U11/U12 snRNP / post-mRNA release spliceosomal complex / 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 / 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 / B-WICH complex / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / miRNA processing / embryonic brain development / protein methylation / U12-type spliceosomal complex / oocyte development / alternative mRNA splicing, via spliceosome / poly(A) binding / 7-methylguanosine cap hypermethylation / RNA splicing, via transesterification reactions / U1 snRNP binding / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / methylosome / blastocyst formation / regulation of mRNA splicing, via spliceosome / pICln-Sm protein complex / C2H2 zinc finger domain binding / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / P granule / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / telomerase holoenzyme complex / U2-type spliceosomal complex / telomerase RNA binding / commitment complex / mRNA cis splicing, via spliceosome / U2-type prespliceosome assembly / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / SAGA complex / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / protein peptidyl-prolyl isomerization / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / inner cell mass cell proliferation / WD40-repeat domain binding / ubiquitin-ubiquitin ligase activity / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / cyclosporin A binding / pattern recognition receptor activity / lipid biosynthetic process / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / regulation of RNA splicing / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Prp19 complex / blastocyst development / protein K63-linked ubiquitination / U5 snRNA binding / U5 snRNP / protein localization to nucleus / positive regulation of G1/S transition of mitotic cell cycle / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / RNA processing / positive regulation of viral genome replication / Cajal body / U1 snRNA binding / regulation of DNA repair / proteasomal protein catabolic process / transcription regulator inhibitor activity / ovarian follicle development / U4/U6 x U5 tri-snRNP complex / spindle assembly / lipid droplet / transcription-coupled nucleotide-excision repair / catalytic step 2 spliceosome / negative regulation of canonical NF-kappaB signal transduction / antiviral innate immune response / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||||||||
![]() | Zhang, X. / Yan, C. / Zhan, X. / Li, L. / Lei, J. / Shi, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 420.9 KB | Display | |
Data in CIF | ![]() | 677.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6890MC ![]() 6889C ![]() 6891C ![]() 5z56C ![]() 5z58C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 15 types, 16 molecules ACbi6JLQNPRTUXYZ
+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 ... , 5 types, 5 molecules KIOVx
+Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy
+Non-polymers , 5 types, 19 molecules 








+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: late Bact splieosome / Type: COMPLEX / Entity ID: #1-#47 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.9 / Details: 20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / 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) |
EM imaging optics | Energyfilter name: GIF Quantum LS |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14316 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Highest resolution: 6.5 Å |