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- PDB-4ab3: ATP-triggered molecular mechanics of the chaperonin GroEL -

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Basic information

Entry
Database: PDB / ID: 4ab3
TitleATP-triggered molecular mechanics of the chaperonin GroEL
Components60 KDA CHAPERONIN
KeywordsCHAPERONE
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
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Chaperonin GroEL
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsClare, D.K. / Vasishtan, D. / Stagg, S. / Quispe, J. / Farr, G.W. / Topf, M. / Horwich, A.L. / Saibil, H.R.
CitationJournal: Cell / Year: 2012
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
DepositionDec 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Other / Structure summary
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description
Category: em_3d_fitting / em_image_scans ...em_3d_fitting / em_image_scans / em_imaging / em_software
Item: _em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max ..._em_3d_fitting.target_criteria / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2003
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Assembly

Deposited unit
A: 60 KDA CHAPERONIN
B: 60 KDA CHAPERONIN
C: 60 KDA CHAPERONIN
D: 60 KDA CHAPERONIN
E: 60 KDA CHAPERONIN
F: 60 KDA CHAPERONIN
G: 60 KDA CHAPERONIN
H: 60 KDA CHAPERONIN
I: 60 KDA CHAPERONIN
J: 60 KDA CHAPERONIN
K: 60 KDA CHAPERONIN
L: 60 KDA CHAPERONIN
M: 60 KDA CHAPERONIN
N: 60 KDA CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)811,63856
Polymers802,86814
Non-polymers8,77042
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
60 KDA CHAPERONIN / HSP60 / GROEL PROTEIN / PROTEIN CPN60


Mass: 57347.703 Da / Num. of mol.: 14 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ATPASE MUTANT, CHAINS A-G ARE IN THE RDOPEN ATP BOUND CONFORMATION. CHAINS H-N ARE IN THE RD5 ATP BOUND CONFORMATION
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GROEL-ATP14 RD5-RDOPEN / Type: COMPLEX
Buffer solutionName: 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
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: 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
MicroscopyModel: FEI TECNAI F20 / Details: THE DATA WERE COLLECTED WITH LEGINON AT SCRIPPS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 148500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 95 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Flex-EMmodel fitting
2NAMD2.6model fitting
3UCSF Chimeramodel fitting
4IMAGIC3D reconstruction
5SPIDER3D reconstruction
CTF correctionDetails: EACH PARTICLE WAS PHASE FLIPPED
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.5 Å / Num. of particles: 15000 / Nominal pixel size: 2.02 Å / Actual pixel size: 2.02 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2003.(DEPOSITION ID: 10412).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1OEL

1oel


Accession code: 1OEL / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.5 Å
Refinement stepCycle: LAST / Highest resolution: 8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53831 0 462 0 54293

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