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- EMDB-1046: ATP-bound states of GroEL captured by cryo-electron microscopy. -

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Basic information

Entry
Database: EMDB / ID: 1046
TitleATP-bound states of GroEL captured by cryo-electron microscopy.
SampleGroES-ADP7-GroEL-ATP7 from E.coli
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataGroEL with GroES and ADP bound to one ring, and ATP bound to the other ring
Methodsingle particle reconstruction, at 23.5 Å resolution
AuthorsSaibil HR
CitationCell, 2001, 107, 869-879

Cell, 2001, 107, 869-879 Yorodumi Papers
ATP-bound states of GroEL captured by cryo-electron microscopy.
N A Ranson / G W Farr / A M Roseman / B Gowen / W A Fenton / A L Horwich / H R Saibil

Validation ReportPDB-ID: 1gru

SummaryFull reportAbout validation report
DateDeposition: Mar 13, 2003 / Header (metadata) release: May 16, 2003 / Map release: May 16, 2003 / Last update: Oct 24, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-1gru
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1046.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.8 Å/pix.
= 358.4 Å
128 pix
2.8 Å/pix.
= 358.4 Å
128 pix
2.8 Å/pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:0.029 (by author), 0.08 (movie #1):
Minimum - Maximum-0.04720771 - 0.27609465
Average (Standard dev.)0.00606513 (0.02973022)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0470.2760.006

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Supplemental data

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Sample components

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Entire GroES-ADP7-GroEL-ATP7 from E.coli

EntireName: GroES-ADP7-GroEL-ATP7 from E.coli
Details: The complexes were prepared by pre-forming a GroEL-GroES-ADP complex, with 100 uM ADP, then adding an excess of single ring GroEL (SR1) to trap any released GroES; then 1 mM ATP was added. Any GroEL-GroES complexes remaining have ADP in the GroES-bound ring and ATP in the other ring, modelling the in vivo ATP-binding reaction.
Oligomeric State: 14-mer / Number of components: 2
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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Component #1: protein, GroEL

ProteinName: GroEL / a.k.a: Chaperonin 60 / Oligomeric Details: 14-mer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 800 kDa / Experimental: 800 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Cell: E. coli

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Component #2: protein, GroES

ProteinName: GroES / a.k.a: Chaperonin 10 / Oligomeric Details: 7-mer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 70 kDa / Experimental: 70 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.8 mg/ml
Buffer solution: 12.5 mM HEPES, 5 mM KCl, 5 mM MgCl2, 100 uM ADP, then 2x molar excess of single ring mutant of GroEL (SR1), then 1 mM ATP just before vitrification. See sample details for an explanation of the experimental design.
pH: 7.5
Support filmholey carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: Blot for 1 second before plunging
Time resolved state: The sample was vitrified within a few seconds of manually mixing in ATP.
Details: Vitrification instrument: self made

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 3000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 105 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 71 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8 / OD range: 1

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1448 / Applied symmetry: C7 (7 fold cyclic)
3D reconstructionAlgorithm: Projection matching / Software: Spider
CTF correction: CTF multiplication and merging of 2D averages
Resolution: 23.5 Å / Resolution method: FSC 0.5
Euler angles: Full coverage around a single axis, using mainly side views
Details: Filtered back projection

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Atomic model buiding

Modeling #1Software: Manual fitting in O / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body. The only movement relative to the crystal structure of GroEL-ES-ADP seen at this resolution is a twist of the free apical domains.
Input PDB model: 1AON
Output model

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