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- PDB-6tmx: Structure of the chaperonin gp146 from the bacteriophage EL (Pseu... -
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Basic information
Entry | Database: PDB / ID: 6tmx | ||||||
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Title | Structure of the chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ATPgammaS | ||||||
![]() | Putative GroEL-like chaperonine protein | ||||||
![]() | CHAPERONE / molecular chaperone / ATPase / chaperonin | ||||||
Function / homology | ![]() mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation ...mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / GroEL-GroES complex / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | ||||||
![]() | Bracher, A. / Wang, H. / Paul, S.S. / Wischnewski, N. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
![]() | ![]() Title: Structure and conformational cycle of a bacteriophage-encoded chaperonin. Authors: Andreas Bracher / Simanta S Paul / Huping Wang / Nadine Wischnewski / F Ulrich Hartl / Manajit Hayer-Hartl / ![]() Abstract: Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key ...Chaperonins are ubiquitous molecular chaperones found in all domains of life. They form ring-shaped complexes that assist in the folding of substrate proteins in an ATP-dependent reaction cycle. Key to the folding cycle is the transient encapsulation of substrate proteins by the chaperonin. Here we present a structural and functional characterization of the chaperonin gp146 (ɸEL) from the phage EL of Pseudomonas aeruginosa. ɸEL, an evolutionarily distant homolog of bacterial GroEL, is active in ATP hydrolysis and prevents the aggregation of denatured protein in a nucleotide-dependent manner. However, ɸEL failed to refold the encapsulation-dependent model substrate rhodanese and did not interact with E. coli GroES, the lid-shaped co-chaperone of GroEL. ɸEL forms tetradecameric double-ring complexes, which dissociate into single rings in the presence of ATP. Crystal structures of ɸEL (at 3.54 and 4.03 Å) in presence of ATP•BeFx revealed two distinct single-ring conformational states, both with open access to the ring cavity. One state showed uniform ATP-bound subunit conformations (symmetric state), whereas the second combined distinct ATP- and ADP-bound subunit conformations (asymmetric state). Cryo-electron microscopy of apo-ɸEL revealed a double-ring structure composed of rings in the asymmetric state (3.45 Å resolution). We propose that the phage chaperonin undergoes nucleotide-dependent conformational switching between double- and single rings and functions in aggregation prevention without substrate protein encapsulation. Thus, ɸEL may represent an evolutionarily more ancient chaperonin prior to acquisition of the encapsulation mechanism. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10530MC ![]() 6tmtC ![]() 6tmuC ![]() 6tmvC ![]() 6tmwC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 61760.941 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-AGS / Has ligand of interest | N | |
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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 |
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Sample preparation
Component | Name: The chaperonin gp146 from the bacteriophage EL (Pseudomonas aeruginosa) in complex with ATPgammaS Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.864 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.125 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot time was 2 sec. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 0.074769 sec. / Electron dose: 1.58 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 732 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 283285 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D7 (2x7 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52885 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: Jelly body refinement D7 symmetry NCS restraints |