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- EMDB-1042: ATP-bound states of GroEL captured by cryo-electron microscopy. -

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Basic information

Entry
Database: EMDB / ID: EMD-1042
TitleATP-bound states of GroEL captured by cryo-electron microscopy.
Map dataThis is a map of the E. coli chaperonin GroEL determined by cryo EM, with no added ligands.
Sample
  • Sample: GroEL chaperonin, unliganded
  • Protein or peptide: GroEL
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / 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 / : / 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 / cytoplasm / 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
Chaperonin GroEL / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.3 Å
AuthorsSaibil HR
CitationJournal: 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.
History
DepositionMar 13, 2003-
Header (metadata) releaseMar 13, 2003-
Map releaseMar 13, 2003-
UpdateOct 30, 2013-
Current statusOct 30, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.19
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1gr5
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1042.gif

Downloads & links

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Map

FileDownload / File: emd_1042.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the E. coli chaperonin GroEL determined by cryo EM, with no added ligands.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 128 pix.
= 222.7 Å		1.74 Å/pix.
x 128 pix.
= 222.7 Å		1.74 Å/pix.
x 128 pix.
= 222.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.73984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.285 / Movie #1: 0.19
Minimum - Maximum-0.31940216 - 0.64586169
Average (Standard dev.)0.02427096 (±0.10151429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 222.69952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.739843751.739843751.73984375
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z222.700222.700222.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.3190.6460.024

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Supplemental data

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Sample components

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Entire : GroEL chaperonin, unliganded

EntireName: GroEL chaperonin, unliganded
Components
  • Sample: GroEL chaperonin, unliganded
  • Protein or peptide: GroEL

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Supramolecule #1000: GroEL chaperonin, unliganded

SupramoleculeName: GroEL chaperonin, unliganded / type: sample / ID: 1000 / Oligomeric state: 14-mer / Number unique components: 1
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: Chaperonin / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Cell: E. coli
Molecular weightExperimental: 800 KDa / Theoretical: 800 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.8 mg/mL
BufferpH: 7.5 / Details: 12.5 mM HEPES, 5 mM KCl, 5 mM MgCl2
GridDetails: holey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self-made / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
TemperatureAverage: 105 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 50 / Average electron dose: 20 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40220 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: CTF multiplication and merging of 2D averages
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Filtered back projection / Number images used: 8728
Final angle assignmentDetails: Full coverage around a single axis, using mainly side views

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Atomic model buiding 1

Initial modelPDB ID:

1der
PDB Unreleased entry

SoftwareName: DockEM
DetailsProtocol: Rigid body. Manual fitting of the 3 domains of a subunit as rigid bodies using O, followed by refinement with DockEM
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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Atomic model buiding 2

Detailspdb entry of the same structure
Output model

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

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