+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34725 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | NPC-trapped pre-60S particle | |||||||||
Map data | NPC-trapped pre-60S particle | |||||||||
Sample |
| |||||||||
Keywords | pre-60S ribosome / RIBOSOME | |||||||||
Function / homology | Function and homology information nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...nuclear RNA export factor complex / regulation of ribosomal subunit export from nucleus / nuclear pore central transport channel / Hydrolases / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / tRNA processing / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / poly(A)+ mRNA export from nucleus / response to cycloheximide / porin activity / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / U5 snRNA binding / regulation of translational fidelity / ribosomal subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / ribosomal small subunit export from nucleus / U1 snRNA binding / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / nucleic acid binding / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / proteolysis / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Li ZQ / Chen SJ / Sui SF | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Nature / Year: 2023 Title: Nuclear export of pre-60S particles through the nuclear pore complex. Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Huiqin Xu / Xiaoyun Yang / Peiyi Wang / Ning Gao / Sen-Fang Sui / Abstract: The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal ...The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34725.map.gz | 1.8 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34725-v30.xml emd-34725.xml | 74.3 KB 74.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34725_fsc.xml | 26.5 KB | Display | FSC data file |
Images | emd_34725.png | 150.2 KB | ||
Others | emd_34725_half_map_1.map.gz emd_34725_half_map_2.map.gz | 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34725 | HTTPS FTP |
-Related structure data
Related structure data | 8hfrMC 8hbnC 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_34725.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | NPC-trapped pre-60S particle | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.668 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: NPC-trapped pre-60S particle half B map
File | emd_34725_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | NPC-trapped pre-60S particle half B map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: NPC-trapped pre-60S particle half A map
File | emd_34725_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | NPC-trapped pre-60S particle half A map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : NPC-trapped pre-60S ribosome
+Supramolecule #1: NPC-trapped pre-60S ribosome
+Macromolecule #1: 60S ribosomal protein L35-A
+Macromolecule #2: 60S ribosomal protein L34-A
+Macromolecule #3: 60S ribosomal protein L29
+Macromolecule #4: 60S ribosomal protein L2-A
+Macromolecule #5: 60S ribosomal protein L23-A
+Macromolecule #6: 60S ribosomal protein L16-A
+Macromolecule #7: 60S ribosomal protein L33-A
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: Nucleolar GTP-binding protein 2
+Macromolecule #10: Nucleolar GTP-binding protein 1
+Macromolecule #11: Ribosome biogenesis protein RLP24
+Macromolecule #12: 60S ribosomal protein L30
+Macromolecule #13: 60S ribosomal protein L3
+Macromolecule #14: Eukaryotic translation initiation factor 6
+Macromolecule #15: 60S ribosomal protein L22-A
+Macromolecule #16: 60S ribosomal protein L31-A
+Macromolecule #17: 60S ribosomal protein L32
+Macromolecule #18: Shuttling pre-60S factor ECM1
+Macromolecule #19: Ribosome biogenesis protein ALB1
+Macromolecule #20: mRNA transport regulator MTR2
+Macromolecule #21: 60S ribosomal protein L13-A
+Macromolecule #22: YEAST 60S ribosomal protein L12-A
+Macromolecule #23: mRNA export factor MEX67
+Macromolecule #24: 60S ribosomal protein L4-A
+Macromolecule #25: 60S ribosomal protein L19-A
+Macromolecule #26: 60S ribosomal protein L14-A
+Macromolecule #27: 60S ribosomal protein L42-A
+Macromolecule #28: Probable metalloprotease ARX1
+Macromolecule #29: 60S ribosomal protein L26-A
+Macromolecule #30: 60S ribosomal export protein NMD3
+Macromolecule #31: 60S ribosomal protein L43-A
+Macromolecule #32: 60S ribosomal protein L20-A
+Macromolecule #33: 60S ribosomal protein L36-A
+Macromolecule #34: 60S ribosomal protein L9-A
+Macromolecule #35: 60S ribosomal protein L25
+Macromolecule #36: Ribosome biogenesis protein NSA2
+Macromolecule #39: Ribosome assembly factor MRT4
+Macromolecule #40: 60S ribosomal protein L37-A
+Macromolecule #41: 60S ribosomal protein L39
+Macromolecule #42: 60S ribosomal protein L8-A
+Macromolecule #43: 60S ribosomal protein L18-A
+Macromolecule #44: 60S ribosomal protein L21-A
+Macromolecule #45: Translation machinery-associated protein 16
+Macromolecule #47: 60S ribosomal protein L15-A
+Macromolecule #48: UPF0642 protein YBL028C
+Macromolecule #49: 60S ribosomal protein L27-A
+Macromolecule #50: 60S ribosomal protein L38
+Macromolecule #51: YEAST 60S ribosomal protein L1-A
+Macromolecule #52: 60S ribosomal protein L7-A
+Macromolecule #53: 60S ribosomal protein L17-A
+Macromolecule #54: 60S ribosomal protein L28
+Macromolecule #55: Bud site selection protein 20
+Macromolecule #56: 60S ribosomal protein L11-A
+Macromolecule #57: 60S ribosomal protein L5
+Macromolecule #37: 25S ribosomal RNA
+Macromolecule #38: 5S ribosomal RNA
+Macromolecule #46: 5.8S ribosomal RNA
+Macromolecule #58: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (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: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |