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- EMDB-6291: 16 Angstrom cryo-EM reconstruction of the alpha, beta, gamma TF55... -

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Basic information

Entry
Database: EMDB / ID: EMD-6291
Title16 Angstrom cryo-EM reconstruction of the alpha, beta, gamma TF55 chaperonin
Map dataCryo-EM reconstruction of the Sulfolobus solfataricus TF55 alpha/beta/gamma chaperonin
Sample
  • Sample: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits
  • Protein or peptide: TF55 chaperonin
KeywordsTF55 chaperonin / protein folding / Sulfolobus solfataricus / cryo-EM
Biological speciesSulfolobus solfataricus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsChaston JJ / Stewart AG / Smits C / Aragao D / Struwe W / Benesch J / Xwong A / Ling M / Ashsan B / Sandin S ...Chaston JJ / Stewart AG / Smits C / Aragao D / Struwe W / Benesch J / Xwong A / Ling M / Ashsan B / Sandin S / Rhodes D / Molugu SK / Bernal RA / Stock D
CitationJournal: Structure / Year: 2016
Title: Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins.
Authors: Jessica J Chaston / Callum Smits / David Aragão / Andrew S W Wong / Bilal Ahsan / Sara Sandin / Sudheer K Molugu / Sanjay K Molugu / Ricardo A Bernal / Daniela Stock / Alastair G Stewart /
Abstract: Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the ...Chaperonins are essential biological complexes assisting protein folding in all kingdoms of life. Whereas homooligomeric bacterial GroEL binds hydrophobic substrates non-specifically, the heterooligomeric eukaryotic CCT binds specifically to distinct classes of substrates. Sulfolobales, which survive in a wide range of temperatures, have evolved three different chaperonin subunits (α, β, γ) that form three distinct complexes tailored for different substrate classes at cold, normal, and elevated temperatures. The larger octadecameric β complexes cater for substrates under heat stress, whereas smaller hexadecameric αβ complexes prevail under normal conditions. The cold-shock complex contains all three subunits, consistent with greater substrate specificity. Structural analysis using crystallography and electron microscopy reveals the geometry of these complexes and shows a novel arrangement of the α and β subunits in the hexadecamer enabling incorporation of the γ subunit.
History
DepositionFeb 28, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseFeb 17, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6291.jpg

Downloads & links

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Map

FileDownload / File: emd_6291.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the Sulfolobus solfataricus TF55 alpha/beta/gamma chaperonin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 160 pix.
= 347.84 Å		2.17 Å/pix.
x 160 pix.
= 347.84 Å		2.17 Å/pix.
x 160 pix.
= 347.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.174 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-4.29047346 - 8.94482517
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-59-59-59
Dimensions160160160
Spacing160160160
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1742.1742.174
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z347.840347.840347.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS-59-59-59
NC/NR/NS160160160
D min/max/mean-4.2908.945-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM reconstruction of the TF55 chaperonin containing the alph...

EntireName: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits
Components
  • Sample: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits
  • Protein or peptide: TF55 chaperonin

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Supramolecule #1000: Cryo-EM reconstruction of the TF55 chaperonin containing the alph...

SupramoleculeName: Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits
type: sample / ID: 1000
Oligomeric state: Octadecamer composed of 6 alpha, 6 beta, and 6 gamma subunits per complex
Number unique components: 1
Molecular weightTheoretical: 1.08 MDa / Method: sequence

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Macromolecule #1: TF55 chaperonin

MacromoleculeName: TF55 chaperonin / type: protein_or_peptide / ID: 1
Details: The TF55 chaperonin is composed of three proteins (alpha, beta, and gamma) arranged in an alternating fashion to form a 9-subunit ring (3 of each protein) which then stacks back-to-back with ...Details: The TF55 chaperonin is composed of three proteins (alpha, beta, and gamma) arranged in an alternating fashion to form a 9-subunit ring (3 of each protein) which then stacks back-to-back with a second ring, forming an 18-subunit complex.
Number of copies: 18 / Oligomeric state: octadecamer / Recombinant expression: Yes
Source (natural)Organism: Sulfolobus solfataricus (archaea) / Strain: DSM1617
Molecular weightTheoretical: 1 MDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pETDUET (Novagen)

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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

Concentration0.5 mg/mL
BufferpH: 8
Details: 20 mM Tris-Cl, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 50 mM NaCl
GridDetails: 400-mesh copper grid with holey carbon film support (Quantifoil R2/2)
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 108 K / Instrument: HOMEMADE PLUNGER
Method: 3 microliters of sample were blotted off the Quantifoil R2/2 grid for 3 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 3200FS
TemperatureMin: 83 K / Max: 103 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification.
Specialist opticsEnergy filter - Name: JEOL in-column / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 20, 2014
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 16534 / Average electron dose: 25 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder: 626 Gatan holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsParticle selection was performed using the e2boxer.py component of the EMAN2. Data was ctf-corrected using the ctfit algorithm and refined using EMAN.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2 / Number images used: 16534
Final two d classificationNumber classes: 100
FSC plot (resolution estimation)

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