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- EMDB-1997: ATP-triggered molecular mechanics of the chaperonin GroEL -

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Basic information

Entry
Database: EMDB / ID: EMD-1997
TitleATP-triggered molecular mechanics of the chaperonin GroEL
Map dataGroEL-Apo
Sample
  • Sample: GroEL
  • Protein or peptide: hsp60
KeywordsTetradecamer of GroEL
Function / homologyChaperonin Cpn60/GroEL/TCP-1 family / protein refolding
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsClare DK / Vasishtan D / Stagg S / Quispe J / Farr GW / Topf M / Horwich AL / Saibil HR
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 1, 2011-
Header (metadata) releaseJan 13, 2012-
Map releaseApr 17, 2012-
UpdateApr 17, 2012-
Current statusApr 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1997.png

Downloads & links

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Map

FileDownload / File: emd_1997.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroEL-Apo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 100 pix.
= 202. Å		2.02 Å/pix.
x 100 pix.
= 202. Å		2.02 Å/pix.
x 100 pix.
= 202. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.28869247 - 3.46702909
Average (Standard dev.)0.06064206 (±0.33465365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 202.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z202.000202.000202.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-2.2893.4670.061

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Supplemental data

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Sample components

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Entire : GroEL

EntireName: GroEL
Components
  • Sample: GroEL
  • Protein or peptide: hsp60

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Supramolecule #1000: GroEL

SupramoleculeName: GroEL / type: sample / ID: 1000 / Oligomeric state: tetradecamer of GroEL / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

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Macromolecule #1: hsp60

MacromoleculeName: 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: Escherichia coli (E. coli) / synonym: E. coli / Location in cell: cytoplasm
Molecular weightExperimental: 56 KDa / Theoretical: 56 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceGO: protein refolding / InterPro: Chaperonin Cpn60/GroEL/TCP-1 family

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.4
Details: 50 mM Tris-HCl pH 7.4, 50 mM KCl and 10 mM MgCl2, 200uM ATP
GridDetails: cflat grids r2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 95 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Timed resolved state: vitrified within 3o seconds / Method: grids were blotted for 2-3 seconds

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 95 K / Max: 95 K / Average: 95 K
DetailsThe data was collected with leginon at SCRIPPS
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were automatically picked using FindEM
CTF correctionDetails: each particle was phase flipped
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC / Details: SIRT was used to reconstruct the final map / Number images used: 1200
Final angle assignmentDetails: theta 80-100, phi 0-51.42

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Atomic model buiding 1

Initial modelPDB ID:

1oel

SoftwareName: Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation coefficient

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