+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35105 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The cryo-EM structure of human pre-Bact complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | spliceosome / pre-Bact complex / RNA splicing / PRP2 / activation / SPLICING | |||||||||
Function / homology | Function and homology information RES complex / 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 ...RES complex / 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 / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / miRNA processing / protein methylation / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / blastocyst formation / U1 snRNP binding / mRNA 3'-end processing / 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 / 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 / transcription regulator inhibitor activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / telomerase RNA binding / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / U2-type catalytic step 2 spliceosome / U4 snRNP / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Notch binding / RUNX3 regulates NOTCH signaling / SAGA complex / U2 snRNP / RHOBTB1 GTPase cycle / positive regulation of mRNA splicing, via spliceosome / Basigin interactions / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / nuclear androgen receptor binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / SMAD binding / regulation of RNA splicing / mRNA 3'-splice site recognition / blastocyst development / protein localization to nucleus / localization / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinoic acid receptor signaling pathway / U5 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / RHOBTB2 GTPase cycle / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / Protein methylation / RNA processing / U2 snRNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified adenovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Zhan X / Lu Y / Shi Y | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Molecular Basis for the activation of Human spliceosome Authors: Zhan X / Lu Y / Shi Y | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_35105.map.gz | 398.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-35105-v30.xml emd-35105.xml | 76.3 KB 76.3 KB | Display Display | EMDB header |
Images | emd_35105.png | 86.4 KB | ||
Filedesc metadata | emd-35105.cif.gz | 21.8 KB | ||
Others | emd_35105_half_map_1.map.gz emd_35105_half_map_2.map.gz | 391.6 MB 391.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35105 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35105 | HTTPS FTP |
-Validation report
Summary document | emd_35105_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_35105_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_35105_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_35105_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35105 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35105 | HTTPS FTP |
-Related structure data
Related structure data | 8i0pMC 8i0rC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_35105.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_35105_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_35105_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : The human pre-Bact complex
+Supramolecule #1: The human pre-Bact complex
+Supramolecule #2: human pre-Bact complex
+Supramolecule #3: pre-mRNA
+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: DNA/RNA-binding protein KIN17
+Macromolecule #12: Cell division cycle 5-like protein
+Macromolecule #13: Protein BUD31 homolog
+Macromolecule #14: Pre-mRNA-splicing factor RBM22
+Macromolecule #15: Spliceosome-associated protein CWC15 homolog
+Macromolecule #16: RNA helicase aquarius
+Macromolecule #17: SNW domain-containing protein 1
+Macromolecule #18: Pleiotropic regulator 1
+Macromolecule #19: Smad nuclear-interacting protein 1
+Macromolecule #20: RNA-binding motif protein, X-linked 2
+Macromolecule #21: BUD13 homolog
+Macromolecule #22: Splicing factor 3B subunit 1
+Macromolecule #23: Splicing factor 3B subunit 3
+Macromolecule #24: U2 small nuclear ribonucleoprotein A'
+Macromolecule #25: U2 small nuclear ribonucleoprotein B''
+Macromolecule #26: Small nuclear ribonucleoprotein Sm D2
+Macromolecule #27: Small nuclear ribonucleoprotein F
+Macromolecule #28: Small nuclear ribonucleoprotein-associated proteins B and B'
+Macromolecule #29: Small nuclear ribonucleoprotein Sm D3
+Macromolecule #30: Small nuclear ribonucleoprotein G
+Macromolecule #31: Small nuclear ribonucleoprotein E
+Macromolecule #32: Small nuclear ribonucleoprotein Sm D1
+Macromolecule #33: Splicing factor 3A subunit 3
+Macromolecule #34: Splicing factor 3A subunit 1
+Macromolecule #35: Splicing factor 3B subunit 2
+Macromolecule #36: Splicing factor 3B subunit 4
+Macromolecule #37: Splicing factor 3B subunit 6
+Macromolecule #38: PHD finger-like domain-containing protein 5A
+Macromolecule #39: Splicing factor 3B subunit 5
+Macromolecule #40: RING-type E3 ubiquitin-protein ligase PPIL2
+Macromolecule #41: Serine/arginine repetitive matrix protein 1
+Macromolecule #42: Peptidyl-prolyl cis-trans isomerase E
+Macromolecule #43: Splicing factor 3A subunit 2
+Macromolecule #44: Unknown polymer
+Macromolecule #2: U5 snRNA
+Macromolecule #6: U6 snRNA
+Macromolecule #7: pre-mRNA
+Macromolecule #8: U2 snRNA
+Macromolecule #45: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #46: MAGNESIUM ION
+Macromolecule #47: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46696 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |