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Open data
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Basic information
Entry | Database: PDB / ID: 7wbb | ||||||
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Title | Cryo-EM structure of substrate engaged Drg1 hexamer | ||||||
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![]() | ATP-binding protein / cryo-EM structure of Drg1 / ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, C.Y. / Wu, D.M. / Chen, Q. / Gao, N. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition. Authors: Chengying Ma / Damu Wu / Qian Chen / Ning Gao / ![]() 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 ...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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 710.2 KB | Display | ![]() |
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PDB format | ![]() | 600.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 32396MC ![]() 7wd3C ![]() 7ykkC ![]() 7yklC ![]() 7yktC ![]() 7ykzC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 84848.742 Da / Num. of mol.: 6 / Mutation: E346Q, E617Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: AFG2 / Production host: ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1975.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ATP / ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Double mutant Drg1 in the presence of ATP with substrate engaged Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification![]() | Cryogen name: ETHANE / Humidity: 100 % |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 8 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: NONE | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152973 / Symmetry type: POINT | ||||||||||||||||||||||||
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