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Yorodumi- EMDB-6721: Cryo-EM structure of the human spliceosome just prior to exon lig... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6721 | |||||||||
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Title | Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom | |||||||||
Map data | Cryo-EM Structure of the Human C* Spliceosome at 3.6 angstrom | |||||||||
Sample |
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Function / homology | Function and homology information second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / spliceosomal complex disassembly / exon-exon junction complex / selenocysteine insertion sequence binding / pre-mRNA 3'-splice site binding / regulation of translation at postsynapse, modulating synaptic transmission ...second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / spliceosomal complex disassembly / exon-exon junction complex / selenocysteine insertion sequence binding / pre-mRNA 3'-splice site binding / regulation of translation at postsynapse, modulating synaptic transmission / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / renal system process / 3'-5' RNA helicase activity / negative regulation of excitatory postsynaptic potential / U2 snRNP binding / alternative mRNA splicing, via spliceosome / intracellular mRNA localization / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / generation of catalytic spliceosome for first transesterification step / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / regulation of vitamin D receptor signaling pathway / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Deadenylation of mRNA / embryonic brain development / negative regulation of phosphorylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / M-decay: degradation of maternal mRNAs by maternally stored factors / Prp19 complex / positive regulation of androgen receptor activity / poly(A) binding / snRNP binding / U1 snRNP binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / embryonic cranial skeleton morphogenesis / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / sno(s)RNA-containing ribonucleoprotein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / commitment complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / RUNX3 regulates NOTCH signaling / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / exploration behavior / U1 snRNP / ubiquitin-ubiquitin ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / lipid biosynthetic process / Cajal body / positive regulation of neurogenesis / U2-type prespliceosome / cyclosporin A binding / nuclear androgen receptor binding / regulation of alternative mRNA splicing, via spliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / retinoic acid receptor signaling pathway / protein kinase inhibitor activity / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) / Human adenovirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhang X / Yan C / Hang J / Finci IL / Lei J / Shi Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell / Year: 2017 Title: An Atomic Structure of the Human Spliceosome. Authors: Xiaofeng Zhang / Chuangye Yan / Jing Hang / Lorenzo I Finci / Jianlin Lei / Yigong Shi / Abstract: Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the ...Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6721.map.gz | 227.2 MB | EMDB map data format | |
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Header (meta data) | emd-6721-v30.xml emd-6721.xml | 68.5 KB 68.5 KB | Display Display | EMDB header |
Images | emd_6721.png | 261.6 KB | ||
Others | emd_6721_half_map_1.map.gz emd_6721_half_map_2.map.gz | 193.4 MB 193.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6721 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6721 | HTTPS FTP |
-Validation report
Summary document | emd_6721_validation.pdf.gz | 889.5 KB | Display | EMDB validaton report |
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Full document | emd_6721_full_validation.pdf.gz | 889 KB | Display | |
Data in XML | emd_6721_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_6721_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6721 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6721 | HTTPS FTP |
-Related structure data
Related structure data | 5xjcMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6721.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM Structure of the Human C* Spliceosome at 3.6 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.338 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_6721_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_6721_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human C* spliceosome
+Supramolecule #1: human C* spliceosome
+Macromolecule #1: Pre-mRNA-processing-splicing factor 8
+Macromolecule #3: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #4: U5 small nuclear ribonucleoprotein 200 kDa helicase
+Macromolecule #5: U5 small nuclear ribonucleoprotein 40 kDa protein
+Macromolecule #9: Pre-mRNA-splicing factor SYF1
+Macromolecule #10: Crooked neck-like protein 1
+Macromolecule #11: Pre-mRNA-splicing factor SPF27
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Pre-mRNA-splicing factor SYF2
+Macromolecule #14: Protein BUD31 homolog
+Macromolecule #15: Pre-mRNA-splicing factor RBM22
+Macromolecule #16: Spliceosome-associated protein CWC15 homolog
+Macromolecule #17: Intron-binding protein aquarius
+Macromolecule #18: SNW domain-containing protein 1
+Macromolecule #19: Peptidyl-prolyl cis-trans isomerase-like 1
+Macromolecule #20: Pleiotropic regulator 1
+Macromolecule #21: Serine/arginine repetitive matrix protein 2
+Macromolecule #22: Pre-mRNA-splicing factor CWC22 homolog
+Macromolecule #23: Pre-mRNA-processing factor 17
+Macromolecule #24: PRKR-interacting protein 1
+Macromolecule #25: ATP-dependent RNA helicase DHX8
+Macromolecule #26: Pre-mRNA-splicing factor SLU7
+Macromolecule #27: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #28: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #29: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #30: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #31: Small nuclear ribonucleoprotein F
+Macromolecule #32: Small nuclear ribonucleoprotein E
+Macromolecule #33: Small nuclear ribonucleoprotein G
+Macromolecule #34: U2 small nuclear ribonucleoprotein A'
+Macromolecule #35: U2 small nuclear ribonucleoprotein B''
+Macromolecule #36: Pre-mRNA-processing factor 19
+Macromolecule #37: Eukaryotic initiation factor 4A-III
+Macromolecule #38: Protein mago nashi homolog 2
+Macromolecule #39: RNA-binding protein 8A
+Macromolecule #40: Protein CASC3
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: pre-mRNA
+Macromolecule #8: Homo sapiens small nuclear RNA (U2) gene
+Macromolecule #41: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #42: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #43: MAGNESIUM ION
+Macromolecule #44: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #45: ZINC ION
+Macromolecule #46: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Chromatic aberration corrector: -10 / Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 10 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-32 / Number grids imaged: 5 / Number real images: 7308 / Average exposure time: 0.25 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 100085 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0) |
Final angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0) |