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- PDB-1gr5: Solution Structure of apo GroEL by Cryo-Electron microscopy -

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Basic information

Entry
Database: PDB / ID: 1gr5
TitleSolution Structure of apo GroEL by Cryo-Electron microscopy
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 / cell cycle / cell division / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
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
Chaperonin GroEL / 60 kDa chaperonin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsRanson, N.A. / Farr, G.W. / Roseman, A.M. / Gowen, B. / Fenton, W.A. / Horwich, A.L. / Saibil, H.R.
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.
#1: Journal: Nature / Year: 1997
Title: The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex.
Authors: Z Xu / A L Horwich / P B Sigler /
Abstract: Chaperonins assist protein folding with the consumption of ATP. They exist as multi-subunit protein assemblies comprising rings of subunits stacked back to back. In Escherichia coli, asymmetric ...Chaperonins assist protein folding with the consumption of ATP. They exist as multi-subunit protein assemblies comprising rings of subunits stacked back to back. In Escherichia coli, asymmetric intermediates of GroEL are formed with the co-chaperonin GroES and nucleotides bound only to one of the seven-subunit rings (the cis ring) and not to the opposing ring (the trans ring). The structure of the GroEL-GroES-(ADP)7 complex reveals how large en bloc movements of the cis ring's intermediate and apical domains enable bound GroES to stabilize a folding chamber with ADP confined to the cis ring. Elevation and twist of the apical domains double the volume of the central cavity and bury hydrophobic peptide-binding residues in the interface with GroES, as well as between GroEL subunits, leaving a hydrophilic cavity lining that is conducive to protein folding. An inward tilt of the cis equatorial domain causes an outward tilt in the trans ring that opposes the binding of a second GroES. When combined with new functional results, this negative allosteric mechanism suggests a model for an ATP-driven folding cycle that requires a double toroid.
#2: Journal: Nat Struct Biol / Year: 1996
Title: The 2.4 A crystal structure of the bacterial chaperonin GroEL complexed with ATP gamma S.
Authors: D C Boisvert / J Wang / Z Otwinowski / A L Horwich / P B Sigler /
Abstract: GroEL is a bacterial chaperonin of 14 identical subunits required to help fold newly synthesized proteins. The crystal structure of GroEL with ATP gamma S bound to each subunit shows that ATP binds ...GroEL is a bacterial chaperonin of 14 identical subunits required to help fold newly synthesized proteins. The crystal structure of GroEL with ATP gamma S bound to each subunit shows that ATP binds to a novel pocket, whose primary sequence is highly conserved among chaperonins. Interaction of Mg2+ and ATP involves phosphate oxygens of the alpha-, beta- and gamma-phosphates, which is unique for known structures of nucleotide-binding proteins. Although bound ATP induces modest conformational shifts in the equatorial domain, the stereochemistry that functionally coordinates GroEL's affinity for nucleotides, polypeptide, and GroES remains uncertain.
#3: Journal: Nature / Year: 1994
Title: The crystal structure of the bacterial chaperonin GroEL at 2.8 A.
Authors: K Braig / Z Otwinowski / R Hegde / D C Boisvert / A Joachimiak / A L Horwich / P B Sigler /
Abstract: The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14 subunits made of two nearly 7-fold rotationally symmetrical rings stacked back-to-back with dyad symmetry. The subunits ...The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14 subunits made of two nearly 7-fold rotationally symmetrical rings stacked back-to-back with dyad symmetry. The subunits consist of three domains: a large equatorial domain that forms the foundation of the assembly at its waist and holds the rings together; a large loosely structured apical domain that forms the ends of the cylinder; and a small slender intermediate domain that connects the two, creating side windows. The three-dimensional structure places most of the mutationally defined functional sites on the channel walls and its outward invaginations, and at the ends of the cylinder.
History
DepositionDec 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Oct 23, 2013Group: Derived calculations
Revision 1.3Aug 19, 2015Group: Other
Revision 1.4Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

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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


Theoretical massNumber of molelcules
Total (without water)800,63814
Polymers800,63814
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41290 Å2
ΔGint-462.2 kcal/mol
Surface area372230 Å2
MethodPQS

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Components

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


Mass: 57188.410 Da / Num. of mol.: 14 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6F6, UniProt: P0A6F5*PLUS
Compound detailsGROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED ...GROEL IS A HOMOOLIGOMER OF FOURTEEN SUBUNITS ARRANGED IN A DOUBLE RING STRUCTURE. ENGINEERED RESIDUE IN CHAIN A, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN B, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN B, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN C, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN C, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN D, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN D, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN E, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN E, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN F, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN F, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN G, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN G, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN H, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN H, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN I, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN I, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN J, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN J, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN K, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN K, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN L, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN L, ALA 126 TO VAL ENGINEERED RESIDUE IN CHAIN M, ARG 13 TO GLY ENGINEERED RESIDUE IN CHAIN M, ALA 126 TO VAL
Sequence detailsMET 1 IN ALL CHAINS HAS BEEN POST-TRANSLATIONALLY REMOVED.

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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: MOLECULAR CHAPERONEChaperone (protein) / Type: COMPLEX
Buffer solutionName: HEPES / pH: 7.5 / Details: HEPES
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE
Crystal grow
*PLUS
Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Date: Feb 1, 1997
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Calibrated magnification: 40200 X / Nominal defocus max: 1900 nm / Nominal defocus min: 800 nm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 50
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DockEMmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: CLASS AVERAGES
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionMethod: MODEL-BASED ANGULAR REFINEMENT / Resolution: 7.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 8728 / Nominal pixel size: 1.82 Å / Actual pixel size: 1.74 Å
Details: THE THREE DOMAINS FROM EACH SUBUNIT (PDB 1DER) WERE FITTED SEPARATELY INTO EM DENSITY OF WILD TYPE UNLIGANDED GROEL. THE MUTATIONS LISTED ARE PRESENT IN THE FITTED COORDINATES AND NOT IN THE ...Details: THE THREE DOMAINS FROM EACH SUBUNIT (PDB 1DER) WERE FITTED SEPARATELY INTO EM DENSITY OF WILD TYPE UNLIGANDED GROEL. THE MUTATIONS LISTED ARE PRESENT IN THE FITTED COORDINATES AND NOT IN THE MOLECULE WHICH GENERATED THE EM MAP. THE QUOTED RESOLUTION IS AT 3SIGMA - THE RESOLUTION AT FSC=0.5 IS 10.8A THIS ENTRY REPRESENTS THE COMPLETE BIOMOLECULE.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1DER

1der
PDB Unreleased entry

RefinementHighest resolution: 7.9 Å
Refinement stepCycle: LAST / Highest resolution: 7.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52668 0 0 0 52668
Refinement
*PLUS
Highest resolution: 7.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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