7WBB | pdb_00007wbb

Cryo-EM structure of substrate engaged Drg1 hexamer

PDB DOI: https://doi.org/10.2210/pdb7WBB/pdb
EM Map EMD-32396: EMDB EMDataResource

Classification: ATP-binding protein
Organism(s): Saccharomyces cerevisiae, Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-12-16 Released: 2022-12-28
Deposition Author(s): Ma, C.Y., Wu, D.M., Chen, Q., Gao, N.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 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

Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.

Ma, C., Wu, D., Chen, Q., Gao, N.

(2022) Nat Commun 13: 6765-6765

PubMed: 36351914 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-34511-2
Primary Citation Related Structures:
7WBB, 7WD3, 7YKK, 7YKL, 7YKT, 7YKZ

PubMed Abstract:
The type II AAA + ATPase Drg1 is a ribosome assembly factor, functioning to release Rlp24 from the pre-60S particle just exported from nucleus, and its activity in can be inhibited by a drug molecule diazaborine. However, molecular mechanisms of Drg1-mediated Rlp24 removal and diazaborine-mediated inhibition are not fully understood. Here, we report Drg1 structures in different nucleotide-binding and benzo-diazaborine treated states. Drg1 hexamers transits between two extreme conformations (planar or helical arrangement of protomers). By forming covalent adducts with ATP molecules in both ATPase domain, benzo-diazaborine locks Drg1 hexamers in a symmetric and non-productive conformation to inhibits both inter-protomer and inter-ring communication of Drg1 hexamers. We also obtained a substrate-engaged mutant Drg1 structure, in which conserved pore-loops form a spiral staircase to interact with the polypeptide through a sequence-independent manner. Structure-based mutagenesis data highlight the functional importance of the pore-loop, the D1-D2 linker and the inter-subunit signaling motif of Drg1, which share similar regulatory mechanisms with p97. Our results suggest that Drg1 may function as an unfoldase that threads a substrate protein within the pre-60S particle.

Organizational Affiliation

State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.

Macromolecule Content

Total Structure Weight: 516.65 kDa
Atom Count: 33,634
Modeled Residue Count: 4,351
Deposited Residue Count: 4,703
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AFG2 isoform 1	A B C [auth D] D [auth E] E [auth F] A, B, C [auth D], D [auth E], E [auth F], G [auth C]	780	Saccharomyces cerevisiae	Mutation(s): 2 Gene Names: AFG2 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
substrate	F [auth H]	23	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth D] 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 C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] 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 C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] 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 D] H [auth A], I [auth A], J [auth B], K [auth B], L [auth D], M [auth D], N [auth E], O [auth E], P [auth F], Q [auth C], R [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-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 D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth C] Focus chain R [auth C] 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 D] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth C] Focus chain R [auth C]