+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-1999 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ATP-triggered molecular mechanics of the chaperonin GroEL | |||||||||
![]() | The GroEL-ATP7 Rs2 map is one of seven maps calculated from a heterogenous sample | |||||||||
![]() |
| |||||||||
![]() | Tetradecamer of GroEL with ATP bound in one ring | |||||||||
Function / homology | ![]() 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 / protein refolding ...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 / protein refolding / response to heat / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Clare DK / Vasishtan D / Stagg S / Quispe J / Farr GW / Topf M / Horwich AL / Saibil HR | |||||||||
![]() | ![]() Title: ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin. Authors: Daniel K Clare / Daven Vasishtan / Scott Stagg / Joel Quispe / George W Farr / Maya Topf / Arthur L Horwich / Helen R Saibil / ![]() Abstract: The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the ...The chaperonin GroEL assists the folding of nascent or stress-denatured polypeptides by actions of binding and encapsulation. ATP binding initiates a series of conformational changes triggering the association of the cochaperonin GroES, followed by further large movements that eject the substrate polypeptide from hydrophobic binding sites into a GroES-capped, hydrophilic folding chamber. We used cryo-electron microscopy, statistical analysis, and flexible fitting to resolve a set of distinct GroEL-ATP conformations that can be ordered into a trajectory of domain rotation and elevation. The initial conformations are likely to be the ones that capture polypeptide substrate. Then the binding domains extend radially to separate from each other but maintain their binding surfaces facing the cavity, potentially exerting mechanical force upon kinetically trapped, misfolded substrates. The extended conformation also provides a potential docking site for GroES, to trigger the final, 100° domain rotation constituting the "power stroke" that ejects substrate into the folding chamber. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 476.4 KB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 11.1 KB 11.1 KB | Display Display | ![]() |
Images | ![]() | 27.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aarMC ![]() 1997C ![]() 1998C ![]() 2000C ![]() 2001C ![]() 2002C ![]() 2003C ![]() 4aaqC ![]() 4aasC ![]() 4aauC ![]() 4ab2C ![]() 4ab3C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The GroEL-ATP7 Rs2 map is one of seven maps calculated from a heterogenous sample | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.02 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : GroEL-ATP7 Rs2
Entire | Name: GroEL-ATP7 Rs2 |
---|---|
Components |
|
-Supramolecule #1000: GroEL-ATP7 Rs2
Supramolecule | Name: GroEL-ATP7 Rs2 / type: sample / ID: 1000 Oligomeric state: tetradecamer of GroEL with 7 ATP molecules bound Number unique components: 2 |
---|---|
Molecular weight | Experimental: 800 KDa / Theoretical: 800 KDa |
-Macromolecule #1: hsp60
Macromolecule | Name: hsp60 / type: protein_or_peptide / ID: 1 / Name.synonym: GroEL / Details: ATPase Mutant, D398A / Number of copies: 14 / Oligomeric state: tetradecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 56 KDa / Theoretical: 56 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | GO: protein refolding / InterPro: Chaperonin Cpn60/GroEL/TCP-1 family |
-Macromolecule #2: ATP
Macromolecule | Name: ATP / type: ligand / ID: 2 / Name.synonym: ATP / Details: ATP is bound to seven subunits of one ring / Recombinant expression: No |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Experimental: 550 Da / Theoretical: 550 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 4 mg/mL |
---|---|
Buffer | pH: 7.4 Details: 50 mM Tris-HCl pH 7.4, 50 mM KCl and 10 mM MgCl2, 200 uM ATP |
Grid | Details: cflat grids r2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 95 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Timed resolved state: vitrified within 30 seconds / Method: grids were blotted for 2-3 seconds |
-
Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Temperature | Min: 95 K / Max: 95 K / Average: 95 K |
Details | The data were collected with leginon at SCRIPPS |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 148500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
-
Image processing
Details | The particles were automatically picked using FindEM |
---|---|
CTF correction | Details: each particle was phase flipped |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC / Details: SIRT was used to reconstruct the final map / Number images used: 5500 |
Final angle assignment | Details: theta 80-100, phi 0-51.42 |