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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1047 | |||||||||
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Title | ATP-bound states of GroEL captured by cryo-electron microscopy. | |||||||||
![]() | GroEL(D398A)-ATP D398A has severely reduced ATPase rate (half time at least 20 min instead of 15 sec for wild type) | |||||||||
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Function / homology | ![]() GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / protein folding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.9 Å | |||||||||
![]() | Saibil HR | |||||||||
![]() | ![]() Title: ATP-bound states of GroEL captured by cryo-electron microscopy. Authors: N A Ranson / G W Farr / A M Roseman / B Gowen / W A Fenton / A L Horwich / H R Saibil / ![]() Abstract: The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously ...The chaperonin GroEL drives its protein-folding cycle by cooperatively binding ATP to one of its two rings, priming that ring to become folding-active upon GroES binding, while simultaneously discharging the previous folding chamber from the opposite ring. The GroEL-ATP structure, determined by cryo-EM and atomic structure fitting, shows that the intermediate domains rotate downward, switching their intersubunit salt bridge contacts from substrate binding to ATP binding domains. These observations, together with the effects of ATP binding to a GroEL-GroES-ADP complex, suggest structural models for the ATP-induced reduction in affinity for polypeptide and for cooperativity. The model for cooperativity, based on switching of intersubunit salt bridge interactions around the GroEL ring, may provide general insight into cooperativity in other ring complexes and molecular machines. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
Images | ![]() | 39.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 247.4 KB | Display | ![]() |
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Full document | ![]() | 246.6 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c7eMC ![]() 1042C ![]() 1046C ![]() 1gr5C ![]() 1gruC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | GroEL(D398A)-ATP D398A has severely reduced ATPase rate (half time at least 20 min instead of 15 sec for wild type) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.94 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : GroEL-ATP from E.coli
Entire | Name: GroEL-ATP from E.coli |
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Components |
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-Supramolecule #1000: GroEL-ATP from E.coli
Supramolecule | Name: GroEL-ATP from E.coli / type: sample / ID: 1000 / Oligomeric state: 14-mer / Number unique components: 1 |
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Molecular weight | Experimental: 800 KDa / Theoretical: 800 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: Chaperonin Details: D398A mutant; The Asp398Ala mutant of GroEL has severely reduced ATPase activity but can support a round of protein folding. Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 800 KDa / Theoretical: 800 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 Details: 12.5 mM HEPES, 5 mM KCl, 5 mM MgCl2, 250 microM ATP |
Grid | Details: holey carbon film |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self made / Method: Blot for 1 second before plunging |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/ST |
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Temperature | Average: 105 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 160 / Average electron dose: 20 e/Å2 / Od range: 1 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 36080 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | Grids were vitrified within 1 minute of mixing ATP with the GroEL mutant |
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CTF correction | Details: CTF multiplication and merging of 2D averages |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Filtered back projection / Number images used: 6404 |
Final angle assignment | Details: Full coverage around a single axis, using mainly side views |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 1der |
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Software | Name: DockEM |
Details | Protocol: Rigid body. Manual fitting of the 3 domains of a subunit as rigid bodies using O, followed by refinement with DockEM |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-2c7e: |