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Yorodumi- EMDB-1066: Three-dimensional structure of a pre-catalytic human spliceosomal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1066 | |||||||||
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Title | Three-dimensional structure of a pre-catalytic human spliceosomal complex B. | |||||||||
Map data | 3D map of the spliceosome (B delta U1) | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 40.0 Å | |||||||||
Authors | Boehringer D / Makarov EM / Sander B / Makarova OV / Kastner B / Luehrmann R / Stark H | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2004 Title: Three-dimensional structure of a pre-catalytic human spliceosomal complex B. Authors: Daniel Boehringer / Evgeny M Makarov / Bjoern Sander / Olga V Makarova / Berthold Kastner / Reinhard Lührmann / Holger Stark / Abstract: Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary ...Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B. | |||||||||
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_1066.map.gz | 956.5 KB | EMDB map data format | |
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Header (meta data) | emd-1066-v30.xml emd-1066.xml | 6.2 KB 6.2 KB | Display Display | EMDB header |
Images | 1066.gif | 7.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1066 | HTTPS FTP |
-Validation report
Summary document | emd_1066_validation.pdf.gz | 208 KB | Display | EMDB validaton report |
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Full document | emd_1066_full_validation.pdf.gz | 207.1 KB | Display | |
Data in XML | emd_1066_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1066 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1066.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of the spliceosome (B delta U1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.66 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 : HeLa human pre-catalytic Spliceosome, B delta U1
Entire | Name: HeLa human pre-catalytic Spliceosome, B delta U1 |
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Components |
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-Supramolecule #1000: HeLa human pre-catalytic Spliceosome, B delta U1
Supramolecule | Name: HeLa human pre-catalytic Spliceosome, B delta U1 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: spliceosome
Supramolecule | Name: spliceosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: ribo nucleo protein complex / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE |
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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: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER |
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