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Yorodumi- PDB-6ah0: The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ah0 | |||||||||
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Title | The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) | |||||||||
Components |
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Keywords | SPLICING / Spliceosome | |||||||||
Function / homology | Function and homology information spliceosomal snRNP complex / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / U4atac snRNP / R-loop processing / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex ...spliceosomal snRNP complex / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / U4atac snRNP / R-loop processing / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / box C/D sno(s)RNA binding / snRNP binding / U6 snRNP / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / dense fibrillar component / 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 / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / protein methylation / U12-type spliceosomal complex / methylosome / P-body assembly / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / blastocyst formation / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / : / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / positive regulation of mRNA splicing, via spliceosome / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / box C/D snoRNP assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / SAGA complex / nuclear-transcribed mRNA catabolic process / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / regulation of RNA splicing / single fertilization / mRNA catabolic process / MLL1 complex / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / regulation of DNA repair / Cajal body / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / RNA processing / ribonucleoprotein complex binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA Splicing - Major Pathway / small-subunit processome / RNA splicing / response to cocaine / helicase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Zhan, X. / Yan, C. / Zhang, X. / Shi, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Res / Year: 2018 Title: Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Authors: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi / Abstract: The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are ...The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (B complex). The pre-B-to-B and B-to-B transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome. | |||||||||
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 | 6ah0.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ah0.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6ah0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/6ah0 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/6ah0 | HTTPS FTP |
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-Related structure data
Related structure data | 9621MC 9624C 6ahdC 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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-Components
+RNA chain , 5 types, 5 molecules BFGHI
+U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules DE
+Small nuclear ribonucleoprotein ... , 6 types, 18 molecules akPbmQclRdnSehTgjV
+Protein , 9 types, 11 molecules fiU6NMOWXAC
+U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules qrstxyz
+U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules op
+Splicing factor 3A subunit ... , 3 types, 3 molecules uvw
+Splicing factor 3B subunit ... , 6 types, 6 molecules 123457
+U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules JKL
+Non-polymers , 3 types, 3 molecules
+Details
-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: Spliceosome / Type: COMPLEX / Entity ID: #1-#43 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.9 |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186162 / Symmetry type: POINT |
Refinement | Highest resolution: 5.7 Å |