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- EMDB-11602: Structure of a human ABCE1-bound 43S pre-initiation complex - Sta... -
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Basic information
Entry | Database: EMDB / ID: EMD-11602 | |||||||||
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Title | Structure of a human ABCE1-bound 43S pre-initiation complex - State III | |||||||||
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Function / homology | ![]() negative regulation of endoribonuclease activity / male germ cell proliferation / CTPase activity / 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 / viral translational termination-reinitiation / HRI-mediated signaling ...negative regulation of endoribonuclease activity / male germ cell proliferation / CTPase activity / 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 / viral translational termination-reinitiation / HRI-mediated signaling / Cellular response to mitochondrial stress / positive regulation of mRNA cis splicing, via spliceosome / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / translation reinitiation / PERK-mediated unfolded protein response / selenocysteine metabolic process / IRES-dependent viral translational initiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / OAS antiviral response / selenocysteine incorporation / eukaryotic 43S preinitiation complex / selenocysteine insertion sequence binding / protein-synthesizing GTPase / 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 / eukaryotic 48S preinitiation complex / response to TNF agonist / positive regulation of base-excision repair / 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 RNA splicing / negative regulation of DNA repair / ribosome disassembly / 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 / 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 / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / 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 / Peptide chain elongation / monocyte chemotaxis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Kratzat H / Mackens-Kiani T / Ameismeier A / Cheng J / Berninghausen O / Becker T / Beckmann R | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes. Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine ...Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine / Thomas Becker / Roland Beckmann / ![]() ![]() Abstract: In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. ...In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 213.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 87.6 KB 87.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 187.1 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 142.2 MB 219.1 MB 223.3 MB 220.2 MB 221.8 MB 216.5 MB 17.9 MB 1.1 MB 8.4 MB 2.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 357.2 KB | Display | ![]() |
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Full document | ![]() | 356.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a09MC ![]() 6zceC ![]() 6zu9C ![]() 6zvjC ![]() 7a1gC 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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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: local resolution filtered map
+Additional map: focused refinement on ABCE1, post-processed map
+Additional map: multi body refinement body 1
+Additional map: multi body refinement body 2
+Additional map: multi body refinement body 3
+Additional map: multi body refinement body 4
+Additional map: post-processed and masked map
+Additional map: focused refinement on ABCE1, local resolution filtered map
+Additional map: focused refinement on TC, local resolution filtered map
+Additional map: focused refinement on TC, local resolution filtered map
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Sample components
+Entire : ABCE1-bound 43S pre-initiation complex
+Supramolecule #1: ABCE1-bound 43S pre-initiation complex
+Macromolecule #1: 40S ribosomal protein SA
+Macromolecule #2: 40S ribosomal protein S3a
+Macromolecule #3: 40S ribosomal protein S2
+Macromolecule #4: 40S ribosomal protein S26
+Macromolecule #5: 40S ribosomal protein S4, X isoform
+Macromolecule #6: 60S ribosomal protein L41
+Macromolecule #7: 40S ribosomal protein S6
+Macromolecule #8: 40S ribosomal protein S7
+Macromolecule #9: 40S ribosomal protein S8
+Macromolecule #10: 40S ribosomal protein S9
+Macromolecule #11: 40S ribosomal protein S11
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S21
+Macromolecule #14: 40S ribosomal protein S15a
+Macromolecule #15: 40S ribosomal protein S24
+Macromolecule #16: 40S ribosomal protein S27
+Macromolecule #17: 40S ribosomal protein S30
+Macromolecule #19: 40S ribosomal protein S17
+Macromolecule #20: 40S ribosomal protein S3
+Macromolecule #21: 40S ribosomal protein S5
+Macromolecule #22: 40S ribosomal protein S10
+Macromolecule #23: 40S ribosomal protein S12
+Macromolecule #24: 40S ribosomal protein S15
+Macromolecule #25: 40S ribosomal protein S16
+Macromolecule #26: 40S ribosomal protein S18
+Macromolecule #27: 40S ribosomal protein S19
+Macromolecule #28: 40S ribosomal protein S20
+Macromolecule #29: 40S ribosomal protein S25
+Macromolecule #30: 40S ribosomal protein S28
+Macromolecule #31: 40S ribosomal protein S29
+Macromolecule #32: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #33: Receptor of activated protein C kinase 1
+Macromolecule #34: 40S ribosomal protein S14
+Macromolecule #35: 40S ribosomal protein S23
+Macromolecule #36: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #37: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #38: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #39: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #40: Eukaryotic translation initiation factor 3 subunit C,Eukaryotic t...
+Macromolecule #41: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #42: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #44: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #45: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #47: ATP-binding cassette sub-family E member 1
+Macromolecule #48: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #49: RNA recognition motif
+Macromolecule #51: Eukaryotic translation initiation factor 2 subunit 2
+Macromolecule #52: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #53: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #54: Eukaryotic translation initiation factor 1
+Macromolecule #18: 18S ribosomal RNA
+Macromolecule #50: tRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: IRON/SULFUR CLUSTER
+Macromolecule #57: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #60: METHIONINE
+Macromolecule #61: GUANOSINE-5'-TRIPHOSPHATE
-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: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |