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- EMDB-2002: ATP-triggered molecular mechanics of the chaperonin GroEL -

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Basic information

Entry
Database: EMDB / ID: EMD-2002
TitleATP-triggered molecular mechanics of the chaperonin GroEL
Map dataGroEL-ATP14 Rd2-Rd4ATP
Sample
  • Sample: GroEL-ATP14 Rd2-Rd4
  • Protein or peptide: hsp60
  • Ligand: ATP
KeywordsTetradecamer of GroEL with ATP bound in both rings
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 / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 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 2, 2011-
Header (metadata) releaseDec 16, 2011-
Map releaseApr 17, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4ab2
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD2002.jpeg

Downloads & links

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Map

FileDownload / File: emd_2002.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroEL-ATP14 Rd2-Rd4ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.02 Å/pix.
x 192 pix.
= 387.84 Å		2.02 Å/pix.
x 192 pix.
= 387.84 Å		2.02 Å/pix.
x 192 pix.
= 387.84 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: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.81677616 - 3.09238482
Average (Standard dev.)0.00852973 (±0.10901058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 387.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z387.840387.840387.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1.8173.0920.009

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Supplemental data

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Sample components

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Entire : GroEL-ATP14 Rd2-Rd4

EntireName: GroEL-ATP14 Rd2-Rd4
Components
  • Sample: GroEL-ATP14 Rd2-Rd4
  • Protein or peptide: hsp60
  • Ligand: ATP

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Supramolecule #1000: GroEL-ATP14 Rd2-Rd4

SupramoleculeName: GroEL-ATP14 Rd2-Rd4 / type: sample / ID: 1000
Oligomeric state: tetradecamer of GroEL with 14 ATP molecules bound
Number unique components: 2
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) / 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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Macromolecule #2: ATP

MacromoleculeName: ATP / type: ligand / ID: 2 / Name.synonym: ATP / Details: ATP is bound to all 14 subunits / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 550 Da / Theoretical: 550 Da

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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, 10 mM MgCl2 and 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 30 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: 8.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IMAGIC / Details: SIRT was used to reconstruct the final map / Number images used: 6500
Final angle assignmentDetails: theta 80-100, phi 0-51.42

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Atomic model buiding 1

Initial modelPDB ID:

1oel

SoftwareName: Chimera, Flex-EM, NAMD2.6
DetailsProtocol: Flexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

PDB-4ab2:
ATP-triggered molecular mechanics of the chaperonin GroEL

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