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Yorodumi- EMDB-6493: Electron cryo-microscopy of bacteriophage EL chaperonin in the AD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6493 | |||||||||
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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 |
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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 | |||||||||
Biological species | Pseudomonas phage EL (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.7 Å | |||||||||
Authors | Molugu SK / Hildenbrand ZL / Morgan DG / Sherman MB / He L / Georgopoulos C / Sernova NV / Kurochkina LP / Mesyanzhinov VV / Miroshnikov KA / Bernal RA | |||||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6493.map.gz | 14.4 MB | EMDB map data format | |
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Header (meta data) | emd-6493-v30.xml emd-6493.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_6493.jpg | 96.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6493 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6493 | HTTPS FTP |
-Validation report
Summary document | emd_6493_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_6493_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_6493_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6493 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6493 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6493.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the bacteriophage phi EL ADP-bound chaperonin conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bacteriphage phi-EL encoded chaperonin in the ADP-bound conformation
Entire | Name: Bacteriphage phi-EL encoded chaperonin in the ADP-bound conformation |
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Components |
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-Supramolecule #1000: Bacteriphage phi-EL encoded chaperonin in the ADP-bound conformation
Supramolecule | Name: Bacteriphage phi-EL encoded chaperonin in the ADP-bound conformation type: sample / ID: 1000 / Oligomeric state: homoheptamer / Number unique components: 1 |
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Molecular weight | Theoretical: 431.7677 KDa |
-Macromolecule #1: phi-EL chaperonin
Macromolecule | Name: phi-EL chaperonin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: Yes |
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Source (natural) | 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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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 |
-Electron microscopy
Microscope | JEOL 3200FS |
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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 |
Electron optics | Calibrated magnification: 69000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.7 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, RELION / Number images used: 18778 |