[English] 日本語
Yorodumi- EMDB-17698: Structure of human 48S translation initiation complex upon transf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17698 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / closed | |||||||||
Function / homology | Function and homology information eukaryotic initiation factor eIF2 binding / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress ...eukaryotic initiation factor eIF2 binding / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / HRI-mediated signaling / Cellular response to mitochondrial stress / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / translation reinitiation / selenocysteine metabolic process / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / regulation of translational initiation in response to stress / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / selenocysteine incorporation / selenocysteine insertion sequence binding / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / GDP-dissociation inhibitor activity / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / monocyte chemotaxis / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
Funding support | Germany, 2 items
| |||||||||
Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_17698.map.gz | 160.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-17698-v30.xml emd-17698.xml | 89.3 KB 89.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17698_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_17698.png | 181.7 KB | ||
Masks | emd_17698_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-17698.cif.gz | 20 KB | ||
Others | emd_17698_additional_1.map.gz emd_17698_additional_2.map.gz emd_17698_additional_3.map.gz emd_17698_additional_4.map.gz emd_17698_half_map_1.map.gz emd_17698_half_map_2.map.gz | 163.4 MB 163.1 MB 162.9 MB 140.9 MB 140.8 MB 141.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17698 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17698 | HTTPS FTP |
-Related structure data
Related structure data | 8pj3MC 17696 17697 17699 17700 17701 19128 8pj1C 8pj2C 8pj4C 8pj5C 8pj6C 8rg0C 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_17698.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_17698_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Human 48S initiation complex 40S-eIF1A-eIF2-eIF3-eIF5-eIF5B-tRNA-...
+Supramolecule #1: Human 48S initiation complex 40S-eIF1A-eIF2-eIF3-eIF5-eIF5B-tRNA-...
+Macromolecule #1: Eukaryotic translation initiation factor 5B
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #7: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #9: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #10: 60S ribosomal protein L41
+Macromolecule #12: 40S ribosomal protein S11
+Macromolecule #13: 40S ribosomal protein S4, X isoform
+Macromolecule #14: 40S ribosomal protein S9
+Macromolecule #15: 40S ribosomal protein S23
+Macromolecule #16: Small ribosomal subunit protein eS30
+Macromolecule #17: 40S ribosomal protein S7
+Macromolecule #18: 40S ribosomal protein S27
+Macromolecule #19: 40S ribosomal protein S13
+Macromolecule #20: 40S ribosomal protein S15a
+Macromolecule #21: 40S ribosomal protein S21
+Macromolecule #22: 40S ribosomal protein S2
+Macromolecule #23: 40S ribosomal protein S17
+Macromolecule #24: 40S ribosomal protein SA
+Macromolecule #25: 40S ribosomal protein S3a
+Macromolecule #26: 40S ribosomal protein S14
+Macromolecule #27: 40S ribosomal protein S26
+Macromolecule #28: 40S ribosomal protein S8
+Macromolecule #29: 40S ribosomal protein S6
+Macromolecule #30: 40S ribosomal protein S24
+Macromolecule #31: 40S ribosomal protein S5
+Macromolecule #32: 40S ribosomal protein S16
+Macromolecule #33: 40S ribosomal protein S3
+Macromolecule #34: 40S ribosomal protein S10
+Macromolecule #35: 40S ribosomal protein S15
+Macromolecule #36: Receptor of activated protein C kinase 1
+Macromolecule #37: 40S ribosomal protein S19
+Macromolecule #38: 40S ribosomal protein S25
+Macromolecule #39: 40S ribosomal protein S18
+Macromolecule #40: 40S ribosomal protein S20
+Macromolecule #41: 40S ribosomal protein S29
+Macromolecule #42: Ubiquitin
+Macromolecule #43: 40S ribosomal protein S12
+Macromolecule #44: 40S ribosomal protein S28
+Macromolecule #45: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #46: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #47: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #48: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #49: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #52: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #53: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #54: Eukaryotic translation initiation factor 5
+Macromolecule #8: mRNA
+Macromolecule #11: 18S rRNA
+Macromolecule #51: Initiator Met-tRNA-i
+Macromolecule #55: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #56: SODIUM ION
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Spherical aberration corrector: Electron-optical aberrations were corrected using a CETCOR Cs-corrector (CEOS, Heidelberg) aligned with the CETCORPLUS 4.6.9 software package (CEOS, Heidelberg). |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |