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- EMDB-2001: ATP-triggered molecular mechanics of the chaperonin GroEL -

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Basic information

Entry
Database: EMDB / ID: 2001
TitleATP-triggered molecular mechanics of the chaperonin GroEL
KeywordsTetradecamer of GroEL with ATP bound in both ring
SampleGroEL-ATP14 Rd1-Rd3
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Synthetic construct
Map dataThe GroEL-ATP14 Rd1-Rd3 map is one of seven maps calculated from a heterogenous sample
Methodsingle particle reconstruction, at 8.5 A resolution
AuthorsClare DK / Vasishtan D / Stagg S / Quispe J / Farr GW / Topf M / Horwich AL / Saibil HR
CitationCell, 2012, 149, 113-123

Cell, 2012, 149, 113-123 StrPapers
ATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.
Daniel K Clare / Daven Vasishtan / Scott Stagg / Joel Quispe / George W Farr / Maya Topf / Arthur L Horwich / Helen R Saibil

DateDeposition: Dec 2, 2011 / Header (metadata) release: Dec 16, 2011 / Map release: Apr 17, 2012 / Last update: Dec 2, 2011

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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-4aau
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_2001.map.gz (map file in CCP4 format, 27649 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
2.02 A/pix
= 387.84 A
192 pix
2.02 A/pix
= 387.84 A
192 pix
2.02 A/pix
= 387.84 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.02 A
Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-1.95698512 - 2.98391771
Average (Standard dev.)0.00926961 (0.1169842)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
CellA=B=C: 387.84 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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-1.9572.9840.009

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Supplemental data

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Sample components

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Entire GroEL-ATP14 Rd1-Rd3

EntireName: GroEL-ATP14 Rd1-Rd3 / Number of components: 2
Oligomeric State: Tetradecamer of GroEL with 14 ATP molecules bound
MassTheoretical: 800 kDa / Experimental: 800 kDa

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Component #1: protein, hsp60

ProteinName: hsp60 / a.k.a: GroEL / Oligomeric Details: tetradecamer / Details: ATPase Mutant, D398A / Number of Copies: 14 / Recombinant expression: Yes
MassTheoretical: 56 kDa / Experimental: 56 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)Location in cell: cytoplasm
External referencesGene Ontology: GO: 0042026 / InterPro: InterPro: 002423

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Component #2: ligand, ATP

LigandName: ATP / a.k.a: ATP / Details: ATP is bound to all 14 subunits / Recombinant expression: No
MassTheoretical: 0.55 kDa / Experimental: 0.55 kDa
SourceSpecies: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 4 mg/ml
Buffer solution: 50 mM Tris-HCl pH 7.4, 50 mM KCl, 10 mM MgCl2 and 200uM ATP
pH: 7.4
Support filmcflat grids r2/2
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 95 K / Humidity: 100 % / Method: grids were blotted for 2-3 seconds / Time resolved state: vitrified within 30 seconds / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Details: The data was collected with leginon at SCRIPPS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 148500 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 95 K ( 95 - 95 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6500
Details: The particles were automatically picked using FindEM
Applied symmetry: C7 (7 fold cyclic)
3D reconstructionAlgorithm: projection matching / Euler angles: theta 80-100, phi 0-51.42 / Software: SPIDER, IMAGIC / CTF correction: each particle was phase flipped / Details: SIRT was used to reconstruct the final map / Resolution: 8.5 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera, Flex-EM, NAMD2.6 / Refinement protocol: flexible / Target criteria: cross-correlation coefficient / Refinement space: REAL / Details: Protocol: Flexible fitting
Input PDB model: 1OEL
Output model

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