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Yorodumi- EMDB-1181: Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1181 | |||||||||
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Title | Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. | |||||||||
Map data | GroEL-ADP7-GroES | |||||||||
Sample |
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Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / protein folding chaperone / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Ranson NA | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2006 Title: Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. Authors: Neil A Ranson / Daniel K Clare / George W Farr / David Houldershaw / Arthur L Horwich / Helen R Saibil / Abstract: The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, ...The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, the so-called cis cavity. Upon ATP hydrolysis within the cis ring, the asymmetric complex becomes able to accept non-native polypeptides and ATP in the open, trans ring. Here we have examined the structural basis for this allosteric switch in activity by cryo-EM and single-particle image processing. ATP hydrolysis does not change the conformation of the cis ring, but its effects are transmitted through an inter-ring contact and cause domain rotations in the mobile trans ring. These rigid-body movements in the trans ring lead to disruption of its intra-ring contacts, expansion of the entire ring and opening of both the nucleotide pocket and the substrate-binding domains, admitting ATP and new substrate protein. | |||||||||
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_1181.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-1181-v30.xml emd-1181.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | 1181.gif | 33.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1181 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1181 | HTTPS FTP |
-Validation report
Summary document | emd_1181_validation.pdf.gz | 249.1 KB | Display | EMDB validaton report |
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Full document | emd_1181_full_validation.pdf.gz | 248.2 KB | Display | |
Data in XML | emd_1181_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1181 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1181 | HTTPS FTP |
-Related structure data
Related structure data | 2c7dMC 1180C 2c7cC C: citing same article (ref.) M: atomic model generated by this map |
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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_1181.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | GroEL-ADP7-GroES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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-ADP7-GroES
Entire | Name: GroEL-ADP7-GroES |
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Components |
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-Supramolecule #1000: GroEL-ADP7-GroES
Supramolecule | Name: GroEL-ADP7-GroES / type: sample / ID: 1000 Oligomeric state: One tetradecamer of GroEL plus one heptamer of GroES Number unique components: 2 |
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Molecular weight | Experimental: 900 KDa / Theoretical: 900 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Details: GroEL D398A / Number of copies: 14 / Oligomeric state: tetradecamer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: GroES
Macromolecule | Name: GroES / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
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 | 1.0 mg/mL |
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Buffer | pH: 7.5 / Details: 12.5 mM HEPES, ph7.5 5mM KCl 5mM MgCl2 |
Grid | Details: 300 mesh Cu grid - holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 100 K / Method: blot for 3-4s before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 66 / Average electron dose: 15 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | manual particle selection |
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CTF correction | Details: full correction on 2D class averages |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 7591 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: URO |
Details | Protocol: rigid body. Seven independent domains (equatorial, intermediate and apical domains of each GroEL ring, plus GroES) |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT |
Output model | PDB-2c7d: |