+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13094 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | EIF6-bound large subunit of the human ribosome | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Ribosome / EIF6 / human / SDS / TRANSLATION | |||||||||
Function / homology | Function and homology information lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex ...lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / TORC2 complex binding / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / A band / regulation of reactive oxygen species metabolic process / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / maturation of 5.8S rRNA / response to aldosterone / retinal ganglion cell axon guidance / homeostatic process / G1 to G0 transition / macrophage chemotaxis / lung morphogenesis / male meiosis I / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / preribosome, large subunit precursor / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / protein-RNA complex assembly / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / embryo implantation / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / cytosolic ribosome assembly / regulation of signal transduction by p53 class mediator / skeletal system development / mRNA 3'-UTR binding / positive regulation of translation / sensory perception of sound / response to insulin / bone development / cellular response to gamma radiation / transcription coactivator binding / cellular response to type II interferon / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / cellular response to UV / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / positive regulation of protein binding / ribosome binding / regulation of translation / heparin binding / retina development in camera-type eye / large ribosomal subunit rRNA binding / 5S rRNA binding / cell body / ribosomal large subunit assembly / spermatogenesis / cytoplasmic translation / defense response to Gram-negative bacterium Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Faille A / Warren AJ | |||||||||
Funding support | United Kingdom, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Structure of human EIF6-bound large ribosomal subunit Authors: Faille A / Warren AJ | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_13094.map.gz | 403.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-13094-v30.xml emd-13094.xml | 57.1 KB 57.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13094_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_13094.png | 70 KB | ||
Filedesc metadata | emd-13094.cif.gz | 13.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13094 | HTTPS FTP |
-Validation report
Summary document | emd_13094_validation.pdf.gz | 549.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_13094_full_validation.pdf.gz | 548.8 KB | Display | |
Data in XML | emd_13094_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_13094_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13094 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13094 | HTTPS FTP |
-Related structure data
Related structure data | 7ow7MC 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_13094.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
+Entire : Human large ribosomal subunit
+Supramolecule #1: Human large ribosomal subunit
+Macromolecule #1: 28S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: 60S ribosomal protein L3 isoform a
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L10-like
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L23a
+Macromolecule #24: 60S ribosomal protein L26
+Macromolecule #25: 60S ribosomal protein L27
+Macromolecule #26: 60S ribosomal protein L27a
+Macromolecule #27: 60S ribosomal protein L29
+Macromolecule #28: 60S ribosomal protein L30
+Macromolecule #29: 60S ribosomal protein L31
+Macromolecule #30: 60S ribosomal protein L32
+Macromolecule #31: 60S ribosomal protein L35a
+Macromolecule #32: 60S ribosomal protein L34
+Macromolecule #33: 60S ribosomal protein L35
+Macromolecule #34: 60S ribosomal protein L36
+Macromolecule #35: 60S ribosomal protein L37
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: 60S ribosomal protein L39
+Macromolecule #38: 60S ribosomal protein L36a
+Macromolecule #39: 60S ribosomal protein L37a
+Macromolecule #40: 60S ribosomal protein L28
+Macromolecule #41: Eukaryotic translation initiation factor 6
+Macromolecule #42: 60S ribosomal protein L23
+Macromolecule #43: 60S ribosomal protein L24
+Macromolecule #44: MAGNESIUM ION
+Macromolecule #45: ZINC ION
+Macromolecule #46: POTASSIUM ION
+Macromolecule #47: SODIUM ION
+Macromolecule #48: BROMIDE ION
+Macromolecule #49: water
-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: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |