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Yorodumi- PDB-7pxc: Substrate-engaged mycobacterial Proteasome-associated ATPase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pxc | ||||||
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Title | Substrate-engaged mycobacterial Proteasome-associated ATPase in complex with open-gate 20S CP - composite map (state A) | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / AAA motor / ATPAse / mycobacterium / proteasome activator / 20S CP | ||||||
Function / homology | Function and homology information ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / zymogen binding / cellular response to nitric oxide / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / zymogen binding / cellular response to nitric oxide / proteasomal ubiquitin-independent protein catabolic process / ATP-dependent peptidase activity / proteasome binding / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process / protein tag activity / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / ATP hydrolysis activity / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å | ||||||
Authors | Jomaa, A. / Kavalchuk, M. / Weber-Ban, E. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. Authors: Mikhail Kavalchuk / Ahmad Jomaa / Andreas U Müller / Eilika Weber-Ban / Abstract: Proteasomes are present in eukaryotes, archaea and Actinobacteria, including the human pathogen Mycobacterium tuberculosis, where proteasomal degradation supports persistence inside the host. In ...Proteasomes are present in eukaryotes, archaea and Actinobacteria, including the human pathogen Mycobacterium tuberculosis, where proteasomal degradation supports persistence inside the host. In mycobacteria and other members of Actinobacteria, prokaryotic ubiquitin-like protein (Pup) serves as a degradation tag post-translationally conjugated to target proteins for their recruitment to the mycobacterial proteasome ATPase (Mpa). Here, we use single-particle cryo-electron microscopy to determine the structure of Mpa in complex with the 20S core particle at an early stage of pupylated substrate recruitment, shedding light on the mechanism of substrate translocation. Two conformational states of Mpa show how substrate is translocated stepwise towards the degradation chamber of the proteasome core particle. We also demonstrate, in vitro and in vivo, the importance of a structural feature in Mpa that allows formation of alternating charge-complementary interactions with the proteasome resulting in radial, rail-guided movements during the ATPase conformational cycle. | ||||||
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 | 7pxc.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pxc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pxc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7pxc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7pxc_validation.xml.gz | 213.1 KB | Display | |
Data in CIF | 7pxc_validation.cif.gz | 332.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/7pxc ftp://data.pdbj.org/pub/pdb/validation_reports/px/7pxc | HTTPS FTP |
-Related structure data
Related structure data | 13697MC 7px9C 7pxaC 7pxbC 7pxdC 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
-Proteasome subunit ... , 2 types, 28 molecules 02468IKOQTXZdfHJLMNPRSUVWYab
#1: Protein | Mass: 26911.039 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: The first 7 residues were removed (open gate proteasome) Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: prcA, Rv2109c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHU1 #4: Protein | Mass: 30332.006 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: prcB, Rv2110c / Production host: Escherichia coli (E. coli) References: UniProt: P9WHT9, proteasome endopeptidase complex |
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-Protein , 2 types, 8 molecules 1ABCDEFG
#2: Protein | Mass: 67487.930 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Details: Mpa C-terminal extension containing GQYL motif which interacts with the proteasome Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: mpa, Rv2115c, MTCY261.11c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WQN5 #3: Protein | | Mass: 7095.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pup, Rv2111c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHN5 |
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-Non-polymers , 3 types, 11 molecules
#5: Chemical | ChemComp-ATP / #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ADP / | |
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-Details
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: Mycobacterial Proteasome-associated ATPase in complex with substrate and open-gate 20SCP Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 1.1 MDa / Experimental value: NO |
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE |
-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 / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 860718 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.84 Å / Resolution method: OTHER / Num. of particles: 48054 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5KWA Accession code: 5KWA / Source name: PDB / Type: experimental model |