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Open data
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Basic information
Entry | Database: PDB / ID: 4aar | ||||||
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Title | ATP-triggered molecular mechanics of the chaperonin GroEL | ||||||
![]() | 60 KDA CHAPERONIN | ||||||
![]() | CHAPERONE | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
![]() | Clare, D.K. / Vasishtan, D. / Stagg, S. / Quispe, J. / Farr, G.W. / Topf, M. / Horwich, A.L. / Saibil, H.R. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 913.2 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1999MC ![]() 1997C ![]() 1998C ![]() 2000C ![]() 2001C ![]() 2002C ![]() 2003C ![]() 4aaqC ![]() 4aasC ![]() 4aauC ![]() 4ab2C ![]() 4ab3C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 57347.703 Da / Num. of mol.: 14 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ATPASE MUTANT, TETRADECAMER OF GROEL WITH ATP BOUND IN ONE RING Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-MG / Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 398 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 398 TO ALA ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: GROEL-ATP7 RS2 / Type: COMPLEX |
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Buffer solution | Name: 50 MM TRIS-HCL PH 7.4, 50 MM KCL AND 10 MM MGCL2, 200 UM ATP pH: 7.4 Details: 50 MM TRIS-HCL PH 7.4, 50 MM KCL AND 10 MM MGCL2, 200 UM ATP |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: VITRIFIED WITH A VITROBOT AT 100 PERCENT HUMIDITY WITH 2-3 SECONDS BLOTTING TIME |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Details: THE DATA WERE COLLECTED WITH LEGINON AT SCRIPPS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 148500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2 mm |
Specimen holder | Temperature: 95 K |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
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Processing
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CTF correction | Details: EACH PARTICLE WAS PHASE FLIPPED | ||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 8 Å / Num. of particles: 5500 / Nominal pixel size: 2.02 Å / Actual pixel size: 2.02 Å Details: CHAINS A-G ARE IN THE RS2 ATP BOUND CONFORMATION. CHAINS H- N ARE IN THE APO CONFORMATION SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1999. (DEPOSITION ID: 10407). Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 1OEL Accession code: 1OEL / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Highest resolution: 8 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8 Å
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