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Yorodumi- EMDB-17699: Structure of human 48S translation initiation complex after eIF5 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17699 | |||||||||
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Title | Structure of human 48S translation initiation complex after eIF5 release (48S-4) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / closed | |||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / 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 ...positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / 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 / negative regulation of translational initiation in response to stress / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / PERK-mediated unfolded protein response / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / IRES-dependent viral translational initiation / regulation of translational initiation in response to stress / translation reinitiation / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / : / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / neural crest cell differentiation / 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 / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / pigmentation / 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 / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / iron-sulfur cluster binding / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / monocyte chemotaxis / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / regulation of cell division / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / 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 / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
Funding support | Germany, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17699.map.gz | 275 MB | EMDB map data format | |
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Header (meta data) | emd-17699-v30.xml emd-17699.xml | 86 KB 86 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17699_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_17699.png | 187.7 KB | ||
Masks | emd_17699_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-17699.cif.gz | 19.6 KB | ||
Others | emd_17699_additional_1.map.gz emd_17699_additional_2.map.gz emd_17699_additional_3.map.gz emd_17699_half_map_1.map.gz emd_17699_half_map_2.map.gz | 163.4 MB 162.4 MB 140.6 MB 140.7 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17699 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17699 | HTTPS FTP |
-Validation report
Summary document | emd_17699_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17699_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17699_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_17699_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17699 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17699 | HTTPS FTP |
-Related structure data
Related structure data | 8pj4MC 8pj1C 8pj2C 8pj3C 8pj5C 8pj6C 8rg0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17699.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.967 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17699_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: eIF2-GDP substate 1 (48S-4-1)
File | emd_17699_additional_1.map | ||||||||||||
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Annotation | eIF2-GDP substate 1 (48S-4-1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: eIF2-GDP substate 2 (48S-4-2)
File | emd_17699_additional_2.map | ||||||||||||
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Annotation | eIF2-GDP substate 2 (48S-4-2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened main map from 3D refinement step
File | emd_17699_additional_3.map | ||||||||||||
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Annotation | Unsharpened main map from 3D refinement step | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17699_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17699_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human 48S initiation complex 40S-eIF1A-eIF2-eIF3-eIF5B-tRNA-Met-mRNA
+Supramolecule #1: Human 48S initiation complex 40S-eIF1A-eIF2-eIF3-eIF5B-tRNA-Met-mRNA
+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 #8: mRNA
+Macromolecule #11: 18S rRNA
+Macromolecule #51: Initiator Met-tRNA-i
+Macromolecule #54: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: SODIUM ION
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |