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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10839 | |||||||||
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Title | Rix1-Rea1 pre-60S particle - full composite structure | |||||||||
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![]() | pre-60S / Biogenesis / LSU / Large subunit / ribosome assembly / RIBOSOME | |||||||||
Function / homology | ![]() rixosome complex / protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / traversing start control point of mitotic cell cycle / nuclear pre-replicative complex / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of DNA-templated DNA replication initiation ...rixosome complex / protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / Hydrolases / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / traversing start control point of mitotic cell cycle / nuclear pre-replicative complex / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of DNA-templated DNA replication initiation / regulation of polysaccharide biosynthetic process / maturation of 5.8S rRNA / transporter complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / lipopolysaccharide transport / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ATPase activator activity / Formation of a pool of free 40S subunits / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Gram-negative-bacterium-type cell outer membrane assembly / ribosomal large subunit export from nucleus / translational elongation / ribosomal subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / maturation of LSU-rRNA / Neutrophil degranulation / translation initiation factor activity / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / cell outer membrane / DNA-templated DNA replication / metallopeptidase activity / rRNA processing / protein transport / ribosome biogenesis / ATPase binding / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / chromatin binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / proteolysis / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Kater L / Beckmann R | |||||||||
![]() | ![]() Title: Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Authors: Kater L / Mitterer V / Thoms M / Cheng J / Berninghausen O / Beckmann R / Hurt E | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 44.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 89.8 KB 89.8 KB | Display Display | ![]() |
Images | ![]() | 31.4 KB | ||
Filedesc metadata | ![]() | 22 KB | ||
Others | ![]() | 716.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 400.2 KB | Display | ![]() |
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Full document | ![]() | 399.8 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ylhMC ![]() 6yleC ![]() 6ylfC ![]() 6ylgC ![]() 6ylxC ![]() 6ylyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_10839_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Rix1-Rea1 pre-60S assembly particle - composite structure of the ...
+Supramolecule #1: Rix1-Rea1 pre-60S assembly particle - composite structure of the ...
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: Probable metalloprotease ARX1
+Macromolecule #5: rRNA-processing protein CGR1
+Macromolecule #6: 60S ribosomal protein L2-A
+Macromolecule #7: 60S ribosomal protein L3
+Macromolecule #8: 60S ribosomal protein L4-A
+Macromolecule #9: 60S ribosomal protein L5
+Macromolecule #10: 60S ribosomal protein L6-A
+Macromolecule #11: 60S ribosomal protein L7-A
+Macromolecule #12: 60S ribosomal protein L8-A
+Macromolecule #13: 60S ribosomal protein L9-A
+Macromolecule #14: Bud site selection protein 20
+Macromolecule #15: 60S ribosomal protein L11-A
+Macromolecule #16: Pre-rRNA-processing protein IPI1
+Macromolecule #17: 60S ribosomal protein L13-A
+Macromolecule #18: 60S ribosomal protein L14-A
+Macromolecule #19: 60S ribosomal protein L15-A
+Macromolecule #20: 60S ribosomal protein L16-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L19-A
+Macromolecule #24: 60S ribosomal protein L20-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L22-A
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: Ribosome assembly factor MRT4
+Macromolecule #29: 60S ribosomal protein L25
+Macromolecule #30: 60S ribosomal protein L26-A
+Macromolecule #31: 60S ribosomal protein L27-A
+Macromolecule #32: 60S ribosomal protein L28
+Macromolecule #33: Nucleolar GTP-binding protein 1
+Macromolecule #34: Ribosome biogenesis protein ALB1
+Macromolecule #35: 60S ribosomal protein L31-A
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L33-A
+Macromolecule #38: 60S ribosomal protein L34-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L36-A
+Macromolecule #41: 60S ribosomal protein L37-A
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: Nucleolar GTP-binding protein 2
+Macromolecule #45: 60S ribosomal protein L30
+Macromolecule #46: 60S ribosomal protein L1-A
+Macromolecule #47: 60S ribosomal protein L43-A
+Macromolecule #48: 60S ribosomal protein L12-A
+Macromolecule #49: Ribosome biogenesis protein NSA2
+Macromolecule #50: Nuclear GTP-binding protein NUG1
+Macromolecule #51: Protein SDA1
+Macromolecule #52: Ribosome biogenesis protein RLP24
+Macromolecule #53: Ribosome assembly protein 4
+Macromolecule #54: Eukaryotic translation initiation factor 6
+Macromolecule #55: UPF0642 protein YBL028C
+Macromolecule #56: Midasin
+Macromolecule #57: Pre-rRNA-processing protein IPI3
+Macromolecule #58: Pre-rRNA-processing protein RIX1
+Macromolecule #59: ZINC ION
+Macromolecule #60: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #61: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||||||||||
Output model | ![]() PDB-6ylh: |