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- EMDB-0191: OBP chaperonin in the ADP-bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-0191
TitleOBP chaperonin in the ADP-bound state
Map dataA symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ADP-bound state.
Sample
  • Complex: OBP chaperonin in complex with ADP
Biological speciesPseudomonas phage OBP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsStanishneva-Konovalova TB / Sokolova OS
Funding support Russian Federation, 2 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research16-04-01587 Russian Federation
Russian Foundation for Basic Research18-04-01281 Russian Federation
CitationJournal: J Struct Biol / Year: 2020
Title: Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin.
Authors: Tatiana B Stanishneva-Konovalova / Pavel I Semenyuk / Lidia P Kurochkina / Evgeny B Pichkur / Alexander L Vasilyev / Mikhail V Kovalchuk / Mikhail P Kirpichnikov / Olga S Sokolova /
Abstract: Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They ...Chaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However, both of these groups do not include recently discovered viral chaperonins. Here, we solved the symmetry-free cryo-EM structures of a single-ring chaperonin encoded by the gene 246 of bacteriophage OBP Pseudomonas fluorescens, in the nucleotide-free, ATPγS-, and ADP-bound states, with resolutions of 4.3 Å, 5.0 Å, and 6 Å, respectively. The structure of OBP chaperonin reveals a unique subunit arrangement, with three pairs of subunits and one unpaired subunit. Each pair combines subunits in two possible conformations, differing in nucleotide-binding affinity. The binding of nucleotides results in the increase of subunits' conformational variability. Due to its unique structural and functional features, OBP chaperonin can represent a new group.
History
DepositionAug 14, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseAug 28, 2019-
UpdateMar 18, 2020-
Current statusMar 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.122
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.122
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0191.png

Downloads & links

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Map

FileDownload / File: emd_0191.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA symmetry-free cryo-EM structure of a single-ring chaperonin encoded by gene 246 of bacteriophage OBP Pseudomonas fluorescens in the ADP-bound state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.79 Å/pix.
x 132 pix.
= 235.752 Å		1.79 Å/pix.
x 132 pix.
= 235.752 Å		1.79 Å/pix.
x 132 pix.
= 235.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.786 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122 / Movie #1: 0.122
Minimum - Maximum-0.092733294 - 0.33609888
Average (Standard dev.)-0.00023552291 (±0.023781769)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions132132132
Spacing132132132
CellA=B=C: 235.752 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7861.7861.786
M x/y/z132132132
origin x/y/z0.0000.0000.000
length x/y/z235.752235.752235.752
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS132132132
D min/max/mean-0.0930.336-0.000

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Supplemental data

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Sample components

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Entire : OBP chaperonin in complex with ADP

EntireName: OBP chaperonin in complex with ADP
Components
  • Complex: OBP chaperonin in complex with ADP

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Supramolecule #1: OBP chaperonin in complex with ADP

SupramoleculeName: OBP chaperonin in complex with ADP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas phage OBP (virus)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 420 KDa

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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

Concentration2.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75955
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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