7Z11 | pdb_00007z11

Structure of substrate bound DRG1 (AFG2)

PDB DOI: https://doi.org/10.2210/pdb7Z11/pdb
EM Map EMD-14437: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae BY4743
Mutation(s): No

Deposited: 2022-02-24 Released: 2022-09-21
Deposition Author(s): Prattes, M., Grishkovskaya, I., Bergler, H., Haselbach, D.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.

Prattes, M., Grishkovskaya, I., Hodirnau, V.V., Hetzmannseder, C., Zisser, G., Sailer, C., Kargas, V., Loibl, M., Gerhalter, M., Kofler, L., Warren, A.J., Stengel, F., Haselbach, D., Bergler, H.

(2022) Nat Struct Mol Biol 29: 942-953

PubMed: 36097293 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-022-00832-5
Primary Citation Related Structures:
7Z11, 7Z34

PubMed Abstract:
The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.

Organizational Affiliation

Institute of Molecular Biosciences, University of Graz, Graz, Austria.

Macromolecule Content

Total Structure Weight: 516.58 kDa
Atom Count: 34,079
Modeled Residue Count: 4,404
Deposited Residue Count: 4,700
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family gene 2 protein	A, B, C, D, E A, B, C, D, E, F	780	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: AFG2, DRG1, YLR397C, L8084.16 EC: 3.6.4.10
UniProt
Find proteins for P32794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32794 Go to UniProtKB: P32794
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32794
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide substrate	G	20	Saccharomyces cerevisiae S288C	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth B] K [auth B] L [auth C] H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth E], Q [auth F], R [auth F]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]