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- EMDB-1397: Multiple states of a nucleotide-bound group 2 chaperonin. -

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Basic information

Entry
Database: EMDB / ID: EMD-1397
TitleMultiple states of a nucleotide-bound group 2 chaperonin.
Map dataReconstruction of the bullet conformation of the M. maripaludis group 2 chaperonin
Sample
  • Sample: cpn60
  • Protein or peptide: cpn60
  • Ligand: ADPAlF3
Function / homologyATP binding
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsClare DK / Stagg S / Quispe J / Farr GW / Horwich AL / Saibil HR
CitationJournal: Structure / Year: 2008
Title: Multiple states of a nucleotide-bound group 2 chaperonin.
Authors: Daniel K Clare / Scott Stagg / Joel Quispe / George W Farr / Arthur L Horwich / Helen R Saibil /
Abstract: Chaperonin action is controlled by cycles of nucleotide binding and hydrolysis. Here, we examine the effects of nucleotide binding on an archaeal group 2 chaperonin. In contrast to the ordered apo ...Chaperonin action is controlled by cycles of nucleotide binding and hydrolysis. Here, we examine the effects of nucleotide binding on an archaeal group 2 chaperonin. In contrast to the ordered apo state of the group 1 chaperonin GroEL, the unliganded form of the homo-16-mer Methanococcus maripaludis group 2 chaperonin is very open and flexible, with intersubunit contacts only in the central double belt of equatorial domains. The intermediate and apical domains are free of contacts and deviate significantly from the overall 8-fold symmetry. Nucleotide binding results in three distinct, ordered 8-fold symmetric conformations--open, partially closed, and fully closed. The partially closed ring encloses a 40% larger volume than does the GroEL-GroES folding chamber, enabling it to encapsulate proteins up to 80 kDa, in contrast to the fully closed form, whose cavities are 20% smaller than those of the GroEL-GroES chamber.
History
DepositionAug 1, 2007-
Header (metadata) releaseAug 2, 2007-
Map releaseApr 15, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.258968303
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.258968303
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1397.gif

Downloads & links

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Map

FileDownload / File: emd_1397.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the bullet conformation of the M. maripaludis group 2 chaperonin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
3.26 Å/pix.
x 100 pix.
= 326. Å		3.26 Å/pix.
x 100 pix.
= 326. Å		3.26 Å/pix.
x 100 pix.
= 326. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.26 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.236 / Movie #1: 0.2589683
Minimum - Maximum-0.419736 - 1.76461
Average (Standard dev.)0.0247321 (±0.141326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 326 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z326.000326.000326.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-50-50-50
NX/NY/NZ100100100
MAP C/R/S213
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.4201.7650.025

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Supplemental data

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Sample components

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Entire : cpn60

EntireName: cpn60
Components
  • Sample: cpn60
  • Protein or peptide: cpn60
  • Ligand: ADPAlF3

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Supramolecule #1000: cpn60

SupramoleculeName: cpn60 / type: sample / ID: 1000 / Oligomeric state: hexadecamer / Number unique components: 2
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa

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Macromolecule #1: cpn60

MacromoleculeName: cpn60 / type: protein_or_peptide / ID: 1 / Name.synonym: cpn60 / Details: chaperonin / Number of copies: 16 / Oligomeric state: hexadecamer / Recombinant expression: Yes
Source (natural)Organism: Methanococcus maripaludis (archaea) / Strain: LL / synonym: M. maripaludis / Location in cell: cytoplasm
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa
Recombinant expressionOrganism: Escherichia coli BL21, DE3 / Recombinant plasmid: pET30b
SequenceGO: ATP binding

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Macromolecule #2: ADPAlF3

MacromoleculeName: ADPAlF3 / type: ligand / ID: 2 / Name.synonym: ADPAlF3 / Details: ATP analogue / Recombinant expression: No
Molecular weightExperimental: 500 Da / Theoretical: 500 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

Concentration3 mg/mL
BufferpH: 7.4
Details: 50mM Tris-HCL, 150mM KCl, 10mM MgCl, 1mM DTT 1mM ADP, 5mMKF, 0.5mM Al
GridDetails: 400 mesh c2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER
Details: Vitrification instrument: vitrobot. vitobot chamber was maintained at 37C
Method: 2 second blot

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 92000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry single tilt holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected by leginon
DateMay 12, 2006
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 531 / Average electron dose: 20 e/Å2 / Details: collected using the Leginon system at Scripps
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: theta 80-100, phi 0-45
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 3751
DetailsWe used FindEM to pick the particle

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Atomic model buiding 1

SoftwareName: URO
DetailsProtocol: rigid body. the domains were separately fitted using pymol and then their postions were refined using URO
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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