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- EMDB-5154: Negative stain EM of the recombinant Acidianus tengchongensis cha... -

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Basic information

Entry
Database: EMDB / ID: EMD-5154
TitleNegative stain EM of the recombinant Acidianus tengchongensis chaperonin beta.
Map dataThis is the negative stain microscopy reconstruction of the recombinant thermosome beta from Acidianus tengchongensis
Sample
  • Sample: Negative stain EM of the recombinant Acidianus tengchongensis chaperonin beta
  • Protein or peptide: rATcpn-beta
KeywordsrATcpn-beta / Group II chaperonin / Thermosome
Biological speciesAcidianus tengchongensis (archaea)
Methodsingle particle reconstruction / negative staining / Resolution: 14.0 Å
AuthorsHuo Y / Hu Z / Zhang K / Wang L / Zhai Y / Zhou Q / Lander G / Zhu J / He Y / Pang X ...Huo Y / Hu Z / Zhang K / Wang L / Zhai Y / Zhou Q / Lander G / Zhu J / He Y / Pang X / Xu W / Bartlam M / Dong Z / Sun F
CitationJournal: Structure / Year: 2010
Title: Crystal structure of group II chaperonin in the open state.
Authors: Yanwu Huo / Zhongjun Hu / Kai Zhang / Li Wang / Yujia Zhai / Qiangjun Zhou / Gabe Lander / Jiang Zhu / Yongzhi He / Xiaoyun Pang / Wei Xu / Mark Bartlam / Zhiyang Dong / Fei Sun /
Abstract: Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle ...Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to a lack of high-resolution structure in the open state. Here, we report the first complete crystal structure of thermosome (rATcpnβ) in the open state from Acidianus tengchongensis. There is a ∼30° rotation of the apical and lid domains compared with the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain, and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpnβ were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from the open to the closed state. Structural comparison as well as protease K digestion indicated only ATP binding without hydrolysis does not induce chamber closure of thermosome.
History
DepositionDec 14, 2009-
Header (metadata) releaseAug 4, 2010-
Map releaseOct 21, 2010-
UpdateOct 21, 2010-
Current statusOct 21, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5154_1.png

Downloads & links

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Map

FileDownload / File: emd_5154.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the negative stain microscopy reconstruction of the recombinant thermosome beta from Acidianus tengchongensis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 160 pix.
= 320. Å		2 Å/pix.
x 160 pix.
= 320. Å		2 Å/pix.
x 160 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.15 / Movie #1: 1
Minimum - Maximum-2.57348 - 4.7008
Average (Standard dev.)0.0479447 (±0.477139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-800-80
Dimensions160160160
Spacing160160160
CellA=B=C: 320 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS0-80-80
NC/NR/NS160160160
D min/max/mean-2.5734.7010.048

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Supplemental data

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Sample components

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Entire : Negative stain EM of the recombinant Acidianus tengchongensis cha...

EntireName: Negative stain EM of the recombinant Acidianus tengchongensis chaperonin beta
Components
  • Sample: Negative stain EM of the recombinant Acidianus tengchongensis chaperonin beta
  • Protein or peptide: rATcpn-beta

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Supramolecule #1000: Negative stain EM of the recombinant Acidianus tengchongensis cha...

SupramoleculeName: Negative stain EM of the recombinant Acidianus tengchongensis chaperonin beta
type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: octadecamer / Number unique components: 18
Molecular weightExperimental: 1.08 MDa / Theoretical: 1.08 MDa

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Macromolecule #1: rATcpn-beta

MacromoleculeName: rATcpn-beta / type: protein_or_peptide / ID: 1 / Name.synonym: chaperonin beta / Number of copies: 18 / Oligomeric state: 18mer / Recombinant expression: Yes
Source (natural)Organism: Acidianus tengchongensis (archaea) / Strain: S5 / Location in cell: cytoplasm
Molecular weightTheoretical: 1.08 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET23b

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 4% w/v uranyl acetate for 25 seconds.
GridDetails: 200 mesh gold grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Sampling interval: 14 µm / Number real images: 100 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 70000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsThe particles were selected by hand.
CTF correctionDetails: each photo
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 2328

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