+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1047 | |||||||||
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Title | ATP-bound states of GroEL captured by cryo-electron microscopy. | |||||||||
Map data | GroEL(D398A)-ATP D398A has severely reduced ATPase rate (half time at least 20 min instead of 15 sec for wild type) | |||||||||
Sample |
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Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.9 Å | |||||||||
Authors | Saibil HR | |||||||||
Citation | Journal: Cell / Year: 2001 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1047.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-1047-v30.xml emd-1047.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | 1047.gif | 39.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1047 | HTTPS FTP |
-Validation report
Summary document | emd_1047_validation.pdf.gz | 247.4 KB | Display | EMDB validaton report |
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Full document | emd_1047_full_validation.pdf.gz | 246.6 KB | Display | |
Data in XML | emd_1047_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1047 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1047 | HTTPS FTP |
-Related structure data
Related structure data | 2c7eMC 1042C 1046C 1gr5C 1gruC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_1047.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: Escherichia coli (E. coli) / Cell: E. coli |
Molecular weight | Experimental: 800 KDa / Theoretical: 800 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |
-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: |