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- EMDB-5396: 9-fold symmetric rATcpn-beta in ATP-binding state -

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Basic information

Entry
Database: EMDB / ID: EMD-5396
Title9-fold symmetric rATcpn-beta in ATP-binding state
Map dataReconstruction of the 9-fold symmetric class of rATcpn-beta in ATP-binding state
Sample
  • Sample: rATcpn-beta in ATP-binding state
  • Protein or peptide: Group II chaperonin beta
KeywordsGroup II chaperonin / thermosome
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily ...Thermosome, archaeal / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / 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
Similarity search - Domain/homology
Biological speciesAcidianus tengchongensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsZhang K / Wang L / Liu YX / Wang X / Gao B / Hu ZJ / Ji G / Chan KY / Schulten K / Dong ZY / Sun F
CitationJournal: Protein Cell / Year: 2013
Title: Flexible interwoven termini determine the thermal stability of thermosomes.
Authors: Kai Zhang / Li Wang / Yanxin Liu / Kwok-Yan Chan / Xiaoyun Pang / Klaus Schulten / Zhiyang Dong / Fei Sun /
Abstract: Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II ...Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II chaperonin assembly and thermal stability is yet to be elucidated. Here, we selected the group II chaperonins (cpn-α and cpn-β), also called thermosomes, from Acidianus tengchongensis and investigated their assembly and thermal stability. We found that the binding of ATP or its analogs contributed to the successful assembly of thermosomes and enhanced their thermal stabilities. Cpn-β is more thermally stable than cpn-α, while the thermal stability of the hetero thermosome cpn-αβ is intermediate. Cryo-electron microscopy reconstructions of cpn-α and cpn-β revealed the interwoven densities of their non-conserved flexible N/C-termini around the equatorial planes. The deletion or swapping of their termini and pH-dependent thermal stability assays revealed the key role of the termini electrostatic interactions in the assembly and thermal stability of the thermosomes.
History
DepositionFeb 7, 2012-
Header (metadata) releaseFeb 16, 2012-
Map releaseAug 7, 2013-
UpdateAug 7, 2013-
Current statusAug 7, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j1f
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5396_1.png

Downloads & links

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Map

FileDownload / File: emd_5396.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the 9-fold symmetric class of rATcpn-beta in ATP-binding state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.87 Å/pix.
x 160 pix.
= 298.56 Å		1.87 Å/pix.
x 160 pix.
= 298.56 Å		1.87 Å/pix.
x 160 pix.
= 298.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.866 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-16.156663890000001 - 17.417850489999999
Average (Standard dev.)-0.13943736 (±1.59905684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 298.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8661.8661.866
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z298.560298.560298.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-16.15717.418-0.139

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Supplemental data

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Sample components

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Entire : rATcpn-beta in ATP-binding state

EntireName: rATcpn-beta in ATP-binding state
Components
  • Sample: rATcpn-beta in ATP-binding state
  • Protein or peptide: Group II chaperonin beta

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Supramolecule #1000: rATcpn-beta in ATP-binding state

SupramoleculeName: rATcpn-beta in ATP-binding state / type: sample / ID: 1000 / Oligomeric state: octadecamer / Number unique components: 1
Molecular weightExperimental: 1.08 MDa / Theoretical: 1.08 MDa

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Macromolecule #1: Group II chaperonin beta

MacromoleculeName: Group II chaperonin beta / type: protein_or_peptide / ID: 1 / Name.synonym: rATcpn-beta / Number of copies: 1 / Oligomeric state: octadecamer / Recombinant expression: Yes
Source (natural)Organism: Acidianus tengchongensis (archaea) / Strain: S5T / synonym: Archaea
Molecular weightExperimental: 1.08 MDa / Theoretical: 1.08 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: PET-23b

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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: 7.5 / Details: 25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl
GridDetails: 400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification
DateDec 28, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 3338 / Average electron dose: 20 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: The whole micrograph
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider,EMAN1.9 / Number images used: 28374

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Atomic model buiding 1

Initial modelPDB ID:

3ko1


Chain - Chain ID: A
SoftwareName: Chimera
DetailsProtocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j1f:
Cryo-EM structure of 9-fold symmetric rATcpn-beta in ATP-binding state

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