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Yorodumi- PDB-6tmf: Structure of an archaeal ABCE1-bound ribosomal post-splitting complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tmf | ||||||
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Title | Structure of an archaeal ABCE1-bound ribosomal post-splitting complex | ||||||
Components |
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Keywords | RIBOSOME / ABC Proteins / Ribosome Recycling / Translation | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / oxidoreductase activity / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / ribosomal small subunit binding / translational termination / translational initiation / ribosome biogenesis / small ribosomal subunit / tRNA binding / oxidoreductase activity / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / iron ion binding / ATP hydrolysis activity / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) Thermococcus celer Vu 13 = JCM 8558 (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Kratzat, H. / Becker, T. / Tampe, R. / Beckmann, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: EMBO J / Year: 2020 Title: Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex. Authors: Elina Nürenberg-Goloub / Hanna Kratzat / Holger Heinemann / André Heuer / Peter Kötter / Otto Berninghausen / Thomas Becker / Robert Tampé / Roland Beckmann / Abstract: Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we ...Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we captured the archaeal 30S ribosome post-splitting complex at 2.8 Å resolution by cryo-electron microscopy. The structure reveals the dynamic behavior of structural motifs unique to ABCE1, which ultimately leads to ribosome splitting. More specifically, we provide molecular details on how conformational rearrangements of the iron-sulfur cluster domain and hinge regions of ABCE1 are linked to closure of its nucleotide-binding sites. The combination of mutational and functional analyses uncovers an intricate allosteric network between the ribosome, regulatory domains of ABCE1, and its two structurally and functionally asymmetric ATP-binding sites. Based on these data, we propose a refined model of how signals from the ribosome are integrated into the ATPase cycle of ABCE1 to orchestrate ribosome recycling. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tmf.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6tmf.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6tmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tmf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6tmf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6tmf_validation.xml.gz | 136.7 KB | Display | |
Data in CIF | 6tmf_validation.cif.gz | 228.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tmf ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tmf | HTTPS FTP |
-Related structure data
Related structure data | 10519MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+30S ribosomal protein ... , 25 types, 25 molecules BCDEFGHIJKLMNOPQRSTUVXYZa
-Protein , 3 types, 3 molecules Wbd
#23: Protein | Mass: 6292.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea) References: UniProt: A0A218P055 |
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#28: Protein | Mass: 13351.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea) References: UniProt: A0A218P167 |
#30: Protein | Mass: 67201.469 Da / Num. of mol.: 1 / Mutation: E238A, E485A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) Gene: SSOP1_0270, SULA_1305, SULB_1306, SULC_1304, SULG_06465, SULH_06465, SULI_06465, SULM_06465, SULN_06465, SULO_06475, SULZ_06710 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3MFT8, UniProt: Q980K5*PLUS |
-RNA chain / Protein/peptide , 2 types, 2 molecules Ac
#1: RNA chain | Mass: 482205.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea) References: GenBank: 1214542111 |
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#29: Protein/peptide | Mass: 5023.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermococcus celer Vu 13 = JCM 8558 (archaea) References: UniProt: A0A218P2S9 |
-Non-polymers , 4 types, 37 molecules
#31: Chemical | ChemComp-MG / #32: Chemical | ChemComp-ZN / #33: Chemical | #34: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 10 |
-Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293010 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.65 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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