- EMDB-6493: Electron cryo-microscopy of bacteriophage EL chaperonin in the AD... -
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Basic information
Entry
Database: EMDB / ID: EMD-6493
Title
Electron cryo-microscopy of bacteriophage EL chaperonin in the ADP-bound conformation
Map data
Reconstruction of the bacteriophage phi EL ADP-bound chaperonin conformation
Sample
Sample: Bacteriphage phi-EL encoded chaperonin in the ADP-bound conformation
Protein or peptide: phi-EL chaperonin
Keywords
chaperonin / phi-EL / protein folding / ADP conformation
Function / homology
Function and homology information
GroEL-GroES complex / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation ...GroEL-GroES complex / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / ATP binding / identical protein binding / metal ion binding Similarity search - Function
Journal: Structure / Year: 2016 Title: Ring Separation Highlights the Protein-Folding Mechanism Used by the Phage EL-Encoded Chaperonin. Authors: Sudheer K Molugu / Zacariah L Hildenbrand / David Gene Morgan / Michael B Sherman / Lilin He / Costa Georgopoulos / Natalia V Sernova / Lidia P Kurochkina / Vadim V Mesyanzhinov / Konstantin ...Authors: Sudheer K Molugu / Zacariah L Hildenbrand / David Gene Morgan / Michael B Sherman / Lilin He / Costa Georgopoulos / Natalia V Sernova / Lidia P Kurochkina / Vadim V Mesyanzhinov / Konstantin A Miroshnikov / Ricardo A Bernal / Abstract: Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly ...Chaperonins are ubiquitous, ATP-dependent protein-folding molecular machines that are essential for all forms of life. Bacteriophage φEL encodes its own chaperonin to presumably fold exceedingly large viral proteins via profoundly different nucleotide-binding conformations. Our structural investigations indicate that ATP likely binds to both rings simultaneously and that a misfolded substrate acts as the trigger for ATP hydrolysis. More importantly, the φEL complex dissociates into two single rings resulting from an evolutionarily altered residue in the highly conserved ATP-binding pocket. Conformational changes also more than double the volume of the single-ring internal chamber such that larger viral proteins are accommodated. This is illustrated by the fact that φEL is capable of folding β-galactosidase, a 116-kDa protein. Collectively, the architecture and protein-folding mechanism of the φEL chaperonin are significantly different from those observed in group I and II chaperonins.
History
Deposition
Oct 21, 2015
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Header (metadata) release
Mar 30, 2016
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Map release
Mar 30, 2016
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Update
Apr 27, 2016
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Current status
Apr 27, 2016
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Organism: Pseudomonas phage EL (virus) / synonym: Bacteriophage EL
Molecular weight
Theoretical: 61.6811 KDa
Recombinant expression
Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET22
Sequence
UniProtKB: Putative GroEL-like chaperonine protein
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
2.5 mg/mL
Buffer
pH: 7.5 Details: 50 mM HEPES, pH 7.5, 150 mM NaCl, 2 mM ADP, 2 mM EDTA
Grid
Details: Quantifoil R2/2 grids glow-discharged in air for 1 minute
Vitrification
Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 2-3 seconds before plunging
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Electron microscopy
Microscope
JEOL 3200FS
Temperature
Min: 88 K / Max: 103 K / Average: 100 K
Date
Aug 1, 2009
Image recording
Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 12 µm / Number real images: 50 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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