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Yorodumi- PDB-7ljf: Cryo-EM structure of the Mpa hexamer in the presence of ATP and t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ljf | |||||||||
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Title | Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate | |||||||||
Components | AAA ATPase forming ring-shaped complexes | |||||||||
Keywords | STRUCTURAL PROTEIN / Mycobacterial proteasomal ATPase / Mycobacterium tuberculosis / structural biology / cryo-EM / ATP-Bound | |||||||||
Function / homology | Function and homology information proteasomal protein catabolic process / proteasome complex / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Yin, Y. / Li, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Biol Chem / Year: 2021 Title: The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome. Authors: Yanting Yin / Amanda Kovach / Hao-Chi Hsu / K Heran Darwin / Huilin Li / Abstract: Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. ...Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1-6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique β-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis-driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its β-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease. | |||||||||
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 | 7ljf.cif.gz | 369.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ljf.ent.gz | 293.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ljf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ljf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ljf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ljf_validation.xml.gz | 59 KB | Display | |
Data in CIF | 7ljf_validation.cif.gz | 88.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/7ljf ftp://data.pdbj.org/pub/pdb/validation_reports/lj/7ljf | HTTPS FTP |
-Related structure data
Related structure data | 23392MC 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
#1: Protein | Mass: 66582.969 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: arc, mpa, DSI38_15585, E5M52_17490, ERS007661_01151, ERS007665_00732, ERS007679_01634, ERS007681_02311, ERS007703_01049, ERS007720_01453, ERS007722_00998, ERS007741_01455, ERS023446_02559, ...Gene: arc, mpa, DSI38_15585, E5M52_17490, ERS007661_01151, ERS007665_00732, ERS007679_01634, ERS007681_02311, ERS007703_01049, ERS007720_01453, ERS007722_00998, ERS007741_01455, ERS023446_02559, ERS024276_00114, ERS027646_02035, ERS027659_02128, ERS027661_00811, ERS075361_03050, ERS094182_01863, F6W99_00704, FRD82_11355, SAMEA2683035_00457 Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A045JPX7 #2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | 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 | Name: Cryo-EM structure of the Mpa hexamer in the presence of ATP and the Pup-FabD substrate Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.39 MDa / Experimental value: YES |
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-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: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345023 / Symmetry type: POINT |