3J15 | pdb_00003j15

Model of ribosome-bound archaeal Pelota and ABCE1

PDB DOI: https://doi.org/10.2210/pdb3J15/pdb
EM Map EMD-2009: EMDB EMDataResource

Classification: TRANSLATION/TRANSPORT PROTEIN
Organism(s): Thermococcus kodakarensis, Pyrococcus furiosus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-12 Released: 2012-02-22
Deposition Author(s): Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.-P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M., Hopfner, K.-P., Green, R., Beckmann, R.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.

Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.-P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M., Hopfner, K.P., Green, R., Beckmann, R.

(2012) Nature 482: 501-506

PubMed: 22358840 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nature10829
Primary Citation Related Structures:
3J15, 3J16

PubMed Abstract:
Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.

Organizational Affiliation

Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany. becker@lmb.uni-muenchen.de

Macromolecule Content

Total Structure Weight: 109.52 kDa
Atom Count: 7,660
Modeled Residue Count: 950
Deposited Residue Count: 950
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein pelota	A	357	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: pelA, TK0964 EC: 3.1
UniProt
Find proteins for Q5JIB9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIB9 Go to UniProtKB: Q5JIB9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JIB9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter ATP-binding protein	B	593	Pyrococcus furiosus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	E [auth B], F [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 6.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-22
Type: Initial release
Version 1.1: 2012-02-29
Changes: Database references
Version 1.2: 2012-03-28
Changes: Database references
Version 1.3: 2012-04-18
Changes: Database references
Version 1.4: 2014-07-23
Changes: Other
Version 1.5: 2017-09-06
Changes: Data collection
Version 1.6: 2018-07-18
Changes: Data collection
Version 1.7: 2018-08-22
Changes: Data collection, Database references, Source and taxonomy, Structure summary
Version 1.8: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary