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Yorodumi- EMDB-1096: Major conformational change in the complex SF3b upon integration ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1096 | |||||||||
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Title | Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. | |||||||||
Map data | Volume file of the native human U11/U12 di-snRNP | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.4 Å | |||||||||
Authors | Golas MM / Sander B / Will CL / Luhrmann R | |||||||||
Citation | Journal: Mol Cell / Year: 2005 Title: Major conformational change in the complex SF3b upon integration into the spliceosomal U11/U12 di-snRNP as revealed by electron cryomicroscopy. Authors: Monika M Golas / Bjoern Sander / Cindy L Will / Reinhard Lührmann / Holger Stark / Abstract: In some eukaryotes, a minor class of introns is removed by the U12-dependent spliceosome, which contains the small nuclear ribonucleoprotein (snRNP) heterodimer U11/U12. The U11/U12 di-snRNP forms a ...In some eukaryotes, a minor class of introns is removed by the U12-dependent spliceosome, which contains the small nuclear ribonucleoprotein (snRNP) heterodimer U11/U12. The U11/U12 di-snRNP forms a molecular bridge that functionally pairs the intron ends of the pre-mRNA. We have determined the three-dimensional (3D) structure of the human U11/U12 di-snRNP by single particle electron cryomicroscopy using angular reconstitution and random conical tilt. SF3b, a heteromeric protein complex functionally important for branch site recognition, was located in the U11/U12 di-snRNP by antibody labeling and by identification of structural domains of SF3b155, SF3b49, and p14. The conformation of SF3b bound to the U11/U12 di-snRNP differs from that of isolated SF3b: upon integration into the di-snRNP, SF3b rearranges into a more open form. The manner in which SF3b is integrated in the U11/U12 di-snRNP has important implications for branch site recognition. Furthermore, a putative model of the pre-mRNA binding to the U11/U12 di-snRNP is proposed. | |||||||||
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_1096.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-1096-v30.xml emd-1096.xml | 6.1 KB 6.1 KB | Display Display | EMDB header |
Images | 1096.gif | 15.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1096 | HTTPS FTP |
-Validation report
Summary document | emd_1096_validation.pdf.gz | 205.9 KB | Display | EMDB validaton report |
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Full document | emd_1096_full_validation.pdf.gz | 205 KB | Display | |
Data in XML | emd_1096_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1096 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1096 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1096.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Volume file of the native human U11/U12 di-snRNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human native U11U12 di-snRNP
Entire | Name: human native U11U12 di-snRNP |
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Components |
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-Supramolecule #1000: human native U11U12 di-snRNP
Supramolecule | Name: human native U11U12 di-snRNP / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 1.3 MDa |
-Supramolecule #1: U11U12 di-snRNP
Supramolecule | Name: U11U12 di-snRNP / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NITROGEN |
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-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.5 CUT-OFF |
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