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- EMDB-5392: 9-fold symmetric rATcpn-alpha in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-5392
Title9-fold symmetric rATcpn-alpha in apo state
Map dataReconstruction of the 9-fold symmetric class of apo rATcpn-alpha
Sample
  • Sample: rATcpn-alpha in apo state
  • Protein or peptide: Group II chaperonin alpha
KeywordsGroup II chaperonin / thermosome
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP 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 / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Chaperonin alpha subunit
Similarity search - Component
Biological speciesAcidianus tengchongensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 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: 1.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j1c
  • Surface level: 1.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5392.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the 9-fold symmetric class of apo rATcpn-alpha
Voxel sizeX=Y=Z: 1.866 Å
Density
Contour LevelBy AUTHOR: 1.8 / Movie #1: 1.8
Minimum - Maximum-7.79642487 - 12.34486961
Average (Standard dev.)-0.00000001 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 268.704 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8661.8661.866
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z268.704268.704268.704
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-7.79612.345-0.000

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Supplemental data

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Sample components

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Entire : rATcpn-alpha in apo state

EntireName: rATcpn-alpha in apo state
Components
  • Sample: rATcpn-alpha in apo state
  • Protein or peptide: Group II chaperonin alpha

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Supramolecule #1000: rATcpn-alpha in apo state

SupramoleculeName: rATcpn-alpha in apo state / type: sample / ID: 1000
Details: This sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles
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 alpha

MacromoleculeName: Group II chaperonin alpha / type: protein_or_peptide / ID: 1 / Name.synonym: rATcpn-alpha / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification
DateJul 23, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 3424 / Average electron dose: 20 e/Å2 / Bits/pixel: 32
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: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider,EMAN1.9 / Number images used: 9596

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Atomic model buiding 1

Initial modelPDB ID:

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-3j1c:
Cryo-EM structure of 9-fold symmetric rATcpn-alpha in apo state

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