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- EMDB-1180: Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes. -

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Basic information

Entry
Database: EMDB / ID: EMD-1180
TitleAllosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
Map dataGroEL-ATP7-GroES complex
Sample
  • Sample: GroEL-ATP7-GroES
  • Protein or peptide: GroEL
  • Protein or peptide: GroES
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding ...GroEL-GroES complex / chaperonin ATPase / virion assembly / : / isomerase activity / protein folding chaperone / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / 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 / GroES-like superfamily
Similarity search - Domain/homology
Chaperonin GroEL / Co-chaperonin GroES
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsRanson NA
CitationJournal: Nat Struct Mol Biol / Year: 2006
Title: Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
Authors: Neil A Ranson / Daniel K Clare / George W Farr / David Houldershaw / Arthur L Horwich / Helen R Saibil /
Abstract: The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, ...The double-ring chaperonin GroEL and its lid-like cochaperonin GroES form asymmetric complexes that, in the ATP-bound state, mediate productive folding in a hydrophilic, GroES-encapsulated chamber, the so-called cis cavity. Upon ATP hydrolysis within the cis ring, the asymmetric complex becomes able to accept non-native polypeptides and ATP in the open, trans ring. Here we have examined the structural basis for this allosteric switch in activity by cryo-EM and single-particle image processing. ATP hydrolysis does not change the conformation of the cis ring, but its effects are transmitted through an inter-ring contact and cause domain rotations in the mobile trans ring. These rigid-body movements in the trans ring lead to disruption of its intra-ring contacts, expansion of the entire ring and opening of both the nucleotide pocket and the substrate-binding domains, admitting ATP and new substrate protein.
History
DepositionNov 18, 2005-
Header (metadata) releaseNov 22, 2005-
Map releaseFeb 14, 2006-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.73
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.73
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2c7c
  • Surface level: 0.73
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1180.gif

Downloads & links

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Map

FileDownload / File: emd_1180.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroEL-ATP7-GroES complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.608 / Movie #1: 0.73
Minimum - Maximum-1.7907 - 2.38213
Average (Standard dev.)0.0641685 (±0.230405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 268.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S213
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1.7912.3820.064

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Supplemental data

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Sample components

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Entire : GroEL-ATP7-GroES

EntireName: GroEL-ATP7-GroES
Components
  • Sample: GroEL-ATP7-GroES
  • Protein or peptide: GroEL
  • Protein or peptide: GroES

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Supramolecule #1000: GroEL-ATP7-GroES

SupramoleculeName: GroEL-ATP7-GroES / type: sample / ID: 1000
Oligomeric state: One tetradecamer of GroEL plus one heptamer of GroES
Number unique components: 2
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa

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Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Details: GroEL D398A / Number of copies: 14 / Oligomeric state: tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: GroES

MacromoleculeName: GroES / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
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

Concentration1.0 mg/mL
BufferpH: 7.5 / Details: 12.5 mM HEPES, ph7.5 5mM KCl 5mM MgCl2
GridDetails: 300 mesh Cu grid - holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 100 K / Timed resolved state: Vitrified within 30s of mixing / Method: blot for 3-4s before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 189 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 50000
Sample stageSpecimen holder: single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Detailsmanual particle selection
CTF correctionDetails: full correction on 2D class averages
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 16281

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Atomic model buiding 1

Initial modelPDB ID:

1pcq

SoftwareName: URO
DetailsProtocol: rigid body. Seven independent domains (equatorial, intermediate and apical domains of each GroEL ring, plus GroES)
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-2c7c:
FITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)

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